P.S. How would I go about testing it using animations? Also, what version of 3ds max do you use? I finally found a trial copy of 3ds max 7 so I could use http://cs.elderscrolls.com/constwiki/index.php/3ds_Max:_Exporting_Rigged_Models tut to try and get it export(civ4 plugin needs v7 I guess). No luck with that though it didn't work
To test with animations, import a kf into max. Some get jumpy though. If you are persistent you can get working by saving and reloading them. but most will import correctly. Or if you want you can paste your outfit into a version of the skeleton.nif and attach a kf in nifskope. Or you can export to a nif and load it in the CS and test anims there or in game. basically at any stage you could be testing the rig job.
Niftools plugin works with nearly all versions of max and gmax.
civ4 plugin works with max v6-8.
anyway you have confused me by saying " I imported the _male skeleton into 3ds(my model already matched it's position). I then reset xform on all objects and then collapsed them all individually. After that I added a skin modifier to each and used the niskindata for each piece(the armor is just made up of existing armor pieces, made by bethesda, slightly modified) from nifskope to select which bones to link the mesh to in 3ds max. "
specifically the bit where you "used" the niskindata in nifskope to select... yeah. You mean you just looked at what bones were in those lists and added the same bones seen there but in the skin modifier for your version of the mesh that is now in a max scene.... right. Now where did the actual rigging happen? You bound the mesh to bones, so technically you rigged it. But there's more to it than adding bones to a list.
oh and just incase you actually did this, your wording is not quite right. you should reset xform individually for each mesh, but now matter how many object you have done that for, you can select all of them and collapse the modifier stack in one go, just rclick>convert to editable poly.
and i just noticed you are using editable mesh. Don't. use editable poly, skin will not correctly update from changes to a editable mesh. But it was made to do so for poly.
Anyway I think you are making mountains out of mole hills. I still don't really know what your problem actually is.
as to that link, the last post in that thread. Anyone who says in step 2 to export your mesh. Then step 4 to import your mesh so it is basically exactly where it was just before you exported it. In a 10 step where 2 of those steps are exactly a waste of time, hasn't really thought it out well. Says as much for the rest of the information.