Sounds like your shooting style is similar to me. I use VATS alot and have trouble hitting stuff with the autos; I carry a semi-auto laser rifle, a sniper rifle, and a 10mm pistol. Concentrate on upgrading your guns for damage (not too hard to do at the weapon bench) and trait yourself for improved VATs performance when possible. Also grenades and other explosives are very powerful so make use of those too.

I've also started carrying a melee weapon since so many enemies close the distance and/or spawn at your feet.

As for the extra guns, scrap them out for mats or sell them off. I have not built much in the way of settlements yet so I've been selling most of my junk to buy ammo. Once you have a "base" you are happy with, you can also store your junk there for future use too.

As for gear, since I joined the BoS I just wear BoS armor; I don't see much of a difference with what I'm wearing, so wear what looks good. If I know I'm in for a tough fight, I'll grab my armor otherwise I let it sit most of the time.

This is what I did with my two PC's. I have one that is military oriented that uses energy weapons. I picked the rifleman perk as he does not use full auto weapons and no pistols. I have a sniper rifle for those long range, general purpose rifle for medium range and a shotgun for CQB. I also invested in demolition perk to make nades. This way I only have to keep up with 2 kinds of ammo, fusion cells and shotgun shells which are both plentiful in the game. I take all the other ammo and weapons I loot for barter.

My 2nd PC is a go at it alone character who specializes in stealth. I invested in the sneak (harder to detect while sneaking), ninja (+ dmg while sneaking), and mister sandman (+ dmg with suppressed weapon)perks. Ninja and sandman perks have damage modifiers that stack on each other along with the commando and rifleman perks I invested in as well. I carry only 2 weapons with this character, a full-auto suppressed 10mm pistol and a suppressed 50 cal bolt action pipe sniper rifle. The 10mm gets dmg modifiers from ninja, sandman, and commando. The .50 gets dmg modifier from rifleman, ninja, and sandman perks. This way I only have to keep up with 2 types of ammo again and can use the other to barter for the ammo I do use.

This is how I like to manage it, there are other ways as well.

Edit: and Gun Nut perk also to mod the weapons.

Shotgun for close combat is very good especially against some of the tougher enemies you will face. It can be good both in and out of VATS.

Gun Nut perk will help you out on improving your guns. If using VATS a lot than you do want a high Perception and Agility and perks that are geared to VATS and AP. Also the other Crafting perks will help out a lot.

I suggest using Semi or Single shot weapons at least at first until you get used to Automatics. The the thing with Autos is that you want to fire in bursts and aim a little bit below the chest since Recoil will likely cause the next few bullets to rise and get a chest or head shot if not using VATS. Also crouching (sneak mode) will help to steady the aim a bit. Automatic Weapons are nice if you are being swarmed and if you have some nice mods on them. The bad thing is that they tend to eat a lot of ammo and in the beginning part of the game ammo is in short supply.

One word of advise. If you store items in the workbench, the system can break them down for the basic materials, steel or wood for instance from guns.

So, what I would do, is to build some wardrobes or a metal chest to store your gear in, until you know what you want to use.

As for crafting, go to the armor or weapons workbench and see what kind of options are available to you. Every mod also shows you how the weapon will change.

Receivers increase damage, help with weapon recoil, but some can also lower the range of the weapon

Scopes will increase the range of a weapon

Stock will also help with recoil and accuracy

Magazines can increase ammo count, but also decrease reload speed

There are a few other options, like increasing rate of fire for instance.

A lot of the mods will also increase the weight of the weapon

Also, you will only have access to a few basic mods, until you raise your Gun Nut perk.

You also need the various components, in order to create mods. Most of them require screws and oil, so make sure to store all your junk in the workbench. The system then will use the components of the various items stored there on any crafting station.

When you craft a mod, it is automatically added onto that weapon and the standard one will be in your inventory. You can store mods in the workbench as well and if you find a gun with a better mod, just apply the standard one to that gun and then you can apply that new mod to your other weapon. Mods are weapon type specific though. Any 10mm mod, should work with all 10mm pistols, while a Pipe Rifle mod will not work on a Combat Rifle (at least that's how I understand it).

Same goes for armor. In order to modify say the leather armor, you will need leather, which you can harvest from various animals (hides), as well as other components.

In order to create better armor, you also need to level up the Armorer perk.

I got both Gun Nut and Armorer at lvl 2 at the moment and was able to create some powerful guns. I have a Scoped Powerful Combat Shotgun that does 75 damage (I'm lvl 15). And I'm using Shadowed (helps with sneak) Leather Armor pieces, some with pockets (increase carry weight, and my chest piece is lined with asbestos, so I won't take fire damage).

The Chemistry Crafting station also uses components stored in your main workbench. You can also use it to combine some basic chems you find and make some powerful ones with it.

Like Buffout and Jet (Buffjet), which slows time, raises your strength and endurance and I think HP or something like that.

I collected a lot of guns at the beginning, but stored them to sell when I finally found a merchant. I actually kept modding my 10mm pistol at first and I still use that, in addition to my shotgun and sniper rifle.

I think the pipe guns are rather weak, but the .38 ammo is plentiful. Maybe they will be better at a higher Gun Nut level, but I rather collect "real" guns, instead of home made ones (like the Combat Shotgun or an actual Sniper Rifle). I did create a powerful pipe gun sniper rifle, but the rate of fire was much too slow.

Just play around with the various options and see what you come up with.

A lot of perks are also related to increasing damage from the various weapons. So, you should decide whether you want to go with automatic weapons or not, since there are 2 different perks for regular weapons and auto weapons (under Agility).

If you're using VATS a lot then pistols will be your best friends, so investing in the Gunslinger perk will serve you well. At the start of the game the 10mm is your best bet, but if you plan on doing the Railroad questline you'll get one that's even better for VATS fairly early on. You might want a shotgun for things like ghouls, and maybe something with a bit more range for when you have time to line up a shot. In that case a few perks in rifleman might come in handy.

Ha. I never thought of that. Have been keeping some heavy ordinance and few old favourites in the workbench.

I wonder if they still exist?

As mentioned several times, you should at least carry 3 guns with you for different sitations with different mods.

I go with a 45. cal Combat Rifle (you'll probably didn't find any at the moment, they dropp around level 10-15) with some mid-range mods, semi-auto and a reflex sight for midrange gun fights. In the beginning, you can take a pipe pistol and attach a larger stock and a long barrel to get some "rifle".

For short range I go with a Combat shotgun, recoil compensating stock and a bayonett and max it's damage for close combat. I don't use melee weapons, because changing guns in a fight often results in your death on higher difficulty or against tougher oponents, so the gun-bash with the shotgun if you emptied your mag/against molerats and roaches is great!

For long range i go with my .50 cal Sniper rifle. Night Vision sights, max damage, muzzle break for recoil, i don't care about supressors^^

All those weapons count as "non automatic rifles" and therefore profit from the perk "Rifleman".

In addition to that, always carry some explosives with you. You will find plenty of them, so use em!

For crafting it all is after preferences. You want more carry weight? Go for pocketed/deep pocketed armor.

You want to be a better ninja? Go for shadowd armor.

And so on...

Edit: Stored armor and weapons in the workbench can't be broken down automatically. Only junk will get scrapped if material is needed!