I've downloaded MakeHuman, but the clothes options are a bit lacking and I obviously need Fragger to animate them and Blender to export textures.

Whats the best way of exporting naked MakeHuman files, and then giving them clothes in another program? Advice in general for how to make characters?

Try Fuse CC, its free and more than enough capabilities to make your own characters.
I've done that, afterwards they can be rigged and animated with Mixamo and downloaded as FBX.
Use 3dsmax to convert them to directx.X and import them in Fragmotion.

Well, this is how far i got, made some characters 'see the attachment', did all the steps but i lack the knowledge on how to get it working so it can be used with GG.

is there a tutorial-or at least a lesson lol- on how to rig a character and set up an FPE? I have the model and the FPX files but now I have zero idea what to do

You can make a decent base file using the lowpoly exporter of makehuman (highpoly will simply be overkill for most systems.)
For that you need to use "proxies" which are named "Rorkimaru's or AscottK". Keep in mind that you can not use the hair or clothes in makehuman...way too many polygons.
...but while there is software like Fuse around nowadays, the only real way to make characters is still modeling them. Using a base mesh is perfectly valid.

Now to rig: you can use the animations from a previous model. This is pretty easy and has somewhat decent results with bipedal/human shaped models.
What you need is your model and an animated 3d model in similar "default pose". You can do this in a program called fragmotion which is the easiest option AFAIK. Other modeling packages offer the function as well.

Tutorial on basic rigging

This is for a gun but the process is the same.

I'm fully aware that this is never easy and pretty frustrating at first... but hey, we are here to help. Once you got that going, we can also look at how to set up an fpe. (Its basically just copying the one from another char and editing some values. Sounds easy but can be quite a lot of guesswork at first. For that we need a rigged and working mesh first though. But if you want to have a look: You can open .fpe files in the standart windows notepad.)



-Wolf

After reading that and watching a few (or twenty) tutorials I understand conceptually how the process works now thankfully, I'm working on re-rigging Class FPSC characters into stock Reloaded animations. I'll probally retexture them too, and post the results.

This is where i got stuck, got to learn how to work with Fragmotion and get the pose right.
After reviewing some characters it is my opinion that the wizard is the best option to use because of it's skeleton, i do not need gun animations, just sword, bow and staf.
My thought is that i can take the animation from this character and export it as bhv in order to merge it with a custom character, would that be right?

I use Fuse (the original from Mixamo, not the new version from Adobe, it just works better for me (new version just stops working for me, won't even launch. It also has fewer options so far; if it works on your machine, go for it!). I don't know if it's still available on Steam though, I doubt it.) Anyway, it is, like Earthling45 said, just an upload and rig and then download as FBX. Rafhalzer has a wonderful tool that pretty much automates the rest. It will automatically add Game Guru animations and if you wish to add custom animations you can (You will need to write your own scripts to make the most of custom animations though). I can literally create a character in Fuse in around an hour (depending on how much I change my mind on each feature), upload it, rig it on Adobe's site, and download it as .FBX, import it into "FBX2GG", export, and have a character ready in less than another 30 minutes. FBX2GG costs around $40, though, but considering the time involved rigging and animating from scratch, it is a steal! Here's a link to the thread that I believe has a place where you can buy it:

https://forum.game-guru.com/thread/215728

EDIT and DISCLAIMER: I am not in any way, shape, or form a paid spokesperson for FBX2GG. I am merely sharing my enthusiasm for an application that has made my life so much more fulfilled, lol.