You didn't tell me if you got your package that you were working on to work finally.
as for questions:
No I don't believe that numbering the bain packages themselves will work in auto-sorting them. that was only implemented for subpackages if I recall correctly. The only thing that was implemented (although I don't use it and I'm not sure it stuck in subsequent versions is creating package.txt file that could be read in the bottom pane. Tell you what a great example of how Wrye implemented this can still be found http://www.tesnexus.com/downloads/file.php?id=22170. That link has mods that wrye repackaged himself.
Actually BAIN makes install order a lot less important because you can right click on any package and change the install order and it will shuffle replacers and other files for you. Some say OBMM is better and BAIN is only great for replacers - well I like replacers and I like being able to shuffle them.
Still having a logic to install order is very important just that with BAIN you do not have to actually install in any sequence. Just that after the packages are in you can then arrange the order you want and it will shuffle all files as you instruct it to. Genius stuff by Wrye I tell you - like all the rest of WB really. You can tell he is a fan of the game and of tinkering with it. Why Bethesda doesn't hire him to work on creating public releases of their launcher/CS is beyond me.
Anyway not sure I can tell you the definitive install order but http://www.gamesas.com/bgsforums/index.php?showtopic=1065266&view=findpost&p=15502609 by drag0ntamer I attempted to discuss how to test different levels of instruction.
If it is any help and if you can make sense of it here is my bain packages list (and by extension my install order):
Bain Packages:000 - DarkDarn_160-BAIN.7z (4F5943F5)001 - Unofficial Patches Compilation-BAIN.7z (230F5EF9)002 - SoundsCompilation-BAIN.7z (246CDEB1)003 - World Textures Compilation-BAIN.7z (13B287B3)004 - All Natural-BAIN.7z (AB600C8B)005 - Sky Compilation-BAIN.7z (8FEE36BE)006 - Enhanced Weather-BAIN.7z (774735A5)007 - Environments Compilation-BAIN.7z (8BDD68DA)008 - Other Replacers-BAIN.7z (61570972)009 - DLCOfficialMods-BAIN.7z (6195B9DE)010 - SM Plugin Refurbishes-BAIN.7z (A5AE3399)011 - Fran 4.5X for FCOM-BAIN.7z (1376F51B)012 - OOO_1.34.XForFCOM.7z (84497E2D)013 - MMM_3.7.X-BAIN.7z (1C4D92A2)014 - OWC_1.085b-BAIN.7z (0C244201)015 - FCOM Supplements-BAIN.7z (E1AFDB44)016 - FCOM_Convergence_Beta9.9-BAIN.7z (BAD9768C)017 - ufcom.7z (62B956CB)018 - FCOM Archery-beta-BAIN.7z (6CCC65EF)019 - Armamentarium Complete-BAIN.7z (F64CB9C9)020 - TamrielTravellers-BAIN.7z (8EF850A0)021 - TNR and NPC New Clothes-BAIN.7z (714BF0F6)022 - Horse Compilation-BAIN.7z (BD31B3B5)023 - World TexturesAddendum-BAIN.7z (0D654F5B)024 - LOD Compilation-BAIN.7z (16705CA7)025 - Ampols Textures-BAIN.7z (D19DCB3E)026 - MALO-BAIN.7z (1BC69142)027 - Cobl- BAIN.7z (62B67B45)028 - Books-BAIN.7z (F4A7F7DE)029 - CURP-BAIN.7z (894C221E)030 - _Mergers-BAIN.7z (B4B297E3)031 - Vanilla Redux-BAIN.7z (A103CD73)032 - Choices and Consequences-BAIN.7z (8ED5AEFD)033 - Fort Akatosh + GoC Redux-BAIN.7z (49E0FDDB)034 - Kragenirs Death Quest-BAIN.7z (5BB92BE1)035 - Black Horse Courier-BAIN.7z (9ED44D06)036 - Bartholm-BAIN.7z (76847EAC)037 - Feudal Empire-BAIN.7z (23687B46)038 - TheElderCouncil-BAIN.7z (CDA188E0)039 - Cyrodiil NPC Remodeling-BAIN.7z (7E128283)040 - Kingdom of Almar-BAIN.7z (3A7700B4)041 - Kvatch Aftermath-BAIN.7z (5BE77261)042 - AyliedSteps-BAIN.7z (643A4BC4)043 - Quest for the Elements-BAIN.7z (90247C57)044 - Mighty Umbra-BAIN.7z (FC22BAE8)045 - Verona House Bloodlines-BAIN.7z (D0BA8AB6)046 - OriginMagesGuild-BAIN.7z (750FF65F)047 - Mannimarco Compilation-BAIN.7z (6BEE1259)048 - TheNecromancer-BAIN.7z (EB1F4619)049 - Simyaz Quests-BAIN.7z (B4F59206)050 - Naked Nord-BAIN.7z (2D253EE9)051 - Dragons-BAIN.7z (45FB99C5)052 - A Saints Tale-BAIN.7z (EEA124D4)053 - CastleRavenpride-BAIN.7z (E8F15FEB)054 - Sentient Weapon II-BAIN.7z (B811FEDF)055 - PainKiller Weapon Quests-BAIN.7z (3431D96A)056 - Ivellon-BAIN.7z (BD21A955)057 - Treasure Maps-BAIN.7z (6FC60869)058 - Gates of Asgard-BAIN.7z (F661675D)059 - Thieves Quests-BAIN.7z (7D372944)060 - Heart of the Dead-BAIN.7z (BA216F44)061 - Return of Shadows-BAIN.7z (1780CE76)062 - Werewolf Compilation-BAIN.7z (437128D5)063 - Paladin Mods-BAIN.7z (20B4D8E8)064 - Horror Mods-BAIN.7z (FB5D53C3)065 - Lost Paladins-BAIN.7z (FA7A0847)066 - Blood and Mud-BAIN.7z (286151B9)067 - Lost Spires-BAIN.7z (AB70C310)068 - Et in Arkay Ego-BAIN.7z (B7AC5BDB)069 - Enhanced Daedric Invasion-BAIN.7z (96FEEF47)070 - Quest_Delayers-25859.zip (3B56D53F)071 - Homes-BAIN.7z (272973AB)072 - Castles-BAIN.7z (9DCEF7B6)073 - Dungeons Project-BAIN.7z (DBC3E81D)074 - Frostcrag Reborn-BAIN.7z (A9835361)075 - Skyrim Improved-BAIN.7z (59BEC7A0)076 - Valenwood Improved-BAIN.7z (4831C472)077 - Unique Landscapes Compilation-BAIN.7z (1DD23F60)078 - Elsweyr-Anequina-BAIN.7z (8E787F42)079 - LOD_Compatibility_1_0-27023.7z (D5DBDE84)080 - Old Crow-BAIN.7z (ED905507)081 - Villages-BAIN.7z (AEBEE654)082 - Sutch Reborn-BAIN.7z (93FD8217)083 - Sutch Reborn8.1-bain.7z (F27596F4)084 - Stirk-BAIN.7z (A2A7CA42)085 - Silgrad Tower-Forgotten Garden-BAIN.7z (7BA26851)086 - Windfall-BAIN.7z (235FC5EB)087 - Cybiades-BAIN.7z (4738C4D4)088 - Kvatch Rebuilt-BAIN.7z (26DEB8FE)089 - RAEVWD-BAIN.7z (1317587E)090 - Magic Compilation I-BAIN.7z (F8230434)091 - Mighty Magic-BAIN.7z (75287662)092 - Supreme Magicka-BAIN.7z (8860F2D6)093 - LAME-BAIN.7z (371BAB83)094 - Magic Compilation II-BAIN.7z (5ED0EBDC)095 - Dark Knight Magic-BAIN.7z (F2B7E4C5)096 - Unique Magic Compilation-BAIN.7z (B9ED6B8F)097 - Sigil Stones-BAIN.7z (BD4AA66C)098 - Vows_and_Covenants-20736.7z (31FAA438)099 - Region Rumare-BAIN.7z (4A8713DE)100 - Better Cities Support Mods-BAIN.7z (B8EAD248)101 - City Mods-BAIN.7z (733A98DE)102 - Open Cities-BAIN.7z (7A95C860)103 - Really Open Cities-BAIN.7z (681E8479)104 - ExtinguishtheLights-BAIN.7z (934956ED)105 - Animated_Window_Lighting_System_-_Meshes_v5-1-5-19628.7z (04E69801)106 - AWLS_-_Brumbek_Mixed_Textures_v5-1-2-19628.7z (0D97C8A1)107 - Lighting Compilation-BAIN.7z (C9C086ED)108 - New Roads and Bridges-BAIN.7z (98F8C13E)109 - RobertsMalev4-BAIN.7z (88C638F4)110 - Demon Race-BAIN.7z (E1F7DB45)111 - Race Balancing Project10.5-BAIN.7z (85D5F867)112 - Race Balancing Project 10,5 - Installation Files Complete.7z (C6DE68EF)113 - RBP Variations-BAIN.7z (6B228C1E)114 - Body Compilation Base-BAIN.7z (8F94BC7C)115 - bgIntegration-BAIN.7z (0F88D1C6)116 - Roberts Female-BAIN.7z (8CA25EE3)117 - EVE Compilation-BAIN.7z (513A8316)118 - HGEC Textures-BAIN.7z (48DEF360)119 - CorePC- Clothing Mods-BAIN.7z (15B21FA5)120 - Animations and Idles-BAIN.7z (2BF84249)121 - Companion Control-BAIN.7z (F3C53498)122 - Companions-BAIN.7z (3BAEF937)123 - Sound Sets_PC-BAIN.7z (64E765AD)124 - Sound Sets_Companion-BAIN.7z (66B4E5D3)125 - Power Attack+Diverse Voices-BAIN.7z (6DB683CA)126 - Wrye Mods-BAIN.7z (4CEC37A4)127 - Oblivifall-BAIN.7z (353B36AA)128 - Alternate Starts-BAIN.7z (9D92FEA4)129 - Leveling Compilation-BAIN.7z (D5D28999)130 - Stealth Compilation-BAIN.7z (FF9AE8EE)131 - Realism Compilation-BAIN.7z (D084AD6C)132 - KuerteeMods-BAIN.7z (B352BC54)133 - Tejon Mods-BAIN.7z (D1DF68F4)134 - Optimizers-BAIN.7z (77A38150)135 - DukePatrick Quests-BAIN.7z (155421FB)136 - DP_Survival-Health Mods-BAIN.7z (8A63C694)137 - DP_Combat Mods-BAIN.7z (2E4B3CF4)138 - Duke Patrick Trainers-BAIN.7z (6C4BDA8D)139 - Combat Compilation-BAIN.7z (A1DC8343)140 - Combat Animations-BAIN.7z (6BE0BC31)141 - Scaling Mods-BAIN.7z (93508907)142 - Super_Hotkeys_054-22326.zip (88D642E8)143 - Super_Hotkeys_053-22326.zip (16530903)144 - Really_Immersive_Messages_V1-32-27720.zip (F7411CC1)145 - Visual Enhancments-BAIN.7z (F183F8AC)146 - Travelers & More People-BAIN.7z (551762A2)147 - Creatures & NPCs Alive-BAIN.7z (444C2A80)148 - Life_Detected_80pak-25204.zip (98BAC2D5)149 - HUD Mods-BAIN.7z (057A02E8)150 - Weapon Mods Quest-BAIN.7z (4E252F67)151 - Armor & Weapon Mods - Buy-BAIN.7z (B83194F3)152 - CEO_Main_1_1-26479.7z (16700CAE)153 - Hotkey Compilation-BAIN.7z (E76D88DA)154 - Multiple_Enchantments_V4_7-9423.zip (C04EF303)155 - Chameleon_Cloak-23788.zip (57E557BE)156 - PRP_main_file-20807.rar (55312046)157 - Enhanced_Key_Functionality-27719.zip (BE7AF0BA)158 - Oblivion_Tournament_v2_1_2-28190.7z (D3F37764)159 - ScrollYesOrNo_1_0-28210.rar (451ADD8A)160 - Auriels Retreat-BAIN.7z (34630316)161 - The_Forbidden_Secret-28525.rar (353E8245)162 - Merge Project External-BAIN.7z (A2B380D9)163 - Merge Project Internal to Cities.7z (7D22D554)164 - ImpeREAL_IC-BAIN.7z (ED0D2026)165 - Oblivion Realm Mods-BAIN.7z (A2A88132)166 - Better_Cities_4-4-1-16513.7z (82168F9B)167 - Better_Cities_Resources_4-3-2-16513.7z (39D2548F)168 - Sailing and Boating-BAIN.7z (139F4D70)169 - AFK_PrayerIdles_1-29038.rar (948F12A9)170 - Tantrivalia-BAIN.7z (27B457C3)171 - Dwemer Technology-BAIN.7z (CB7CC8C5)172 - Dragon Paths-BAIN.7z (39580B0E)173 - Daggerfall_NPCs-29161.7z (C1C27F9D)174 - Improved Infrastructure-BAIN.7z (7908F1C6)175 - Merge Project External - No patches.7z (5DE1A33E)176 - Tamriel Houses-BAIN.7z (0F308C2A)177 - Tamriel Houses Other-BAIN.7z (4DF3B742)178 - CLShade Mods-BAIN.7z (F359E6D4)179 - ==Last==180 - WAC-BAIN.7z (BCE82F94)181 - MainMenuVideoReplacements-BAIN.7z (306F12C5)182 - music-24160.rar (9FC93098)183 - CaveExterior_Re-PyFFI.7z (C5B475B3)184 - CyrodiilUpgradeOverhaul-BAIN.7z (01CC96F6)185 - SM_TIE4MODS-BAIN.7z (A3D5FB9B)186 - TIE_In_1_2_beta_3-18071.7z (23623475)187 - UnnecessaryViolence-BAIN.7z (832269C8)188 - Merged Maps-BAIN.7z (91C414B7)189 - Hackdirt-BAIN.7z (21155933)
Mind you that many are not installed (the list packages does not tell you what is installed versus not installed). Some I have just archived, some I plan to use, some I just wanted to test and see. Near the end is where you see less packages and mods that are installed.