Well It appears I fixed it, I'm not even 100% sure how but I'll edit this in a minute with roughly what I did in case someone in future hits the same issue. Thanks everyone especially hishutup for your support, really pushed me in the right direction to help me figure this out.
Edit: So as I found on a sticky on the Skyre compatability patch mod page I attempted to edit all the files with TES5Edit to make it work and I think I did it wrong, so i completely uninstalled the patcher and any reproccer files, then I reinstalled the original reproccer file from Skyre, then installed the reproccer again and ran it all through.
Then on a wim before adding the other compatability patches I went back and reinstalled weapons and armor fixes making sure I did it correctly to work with closefaced helmets. Then I realised I forgot to change the esps for ICFH to optional so I did that, rebuilt everything and it worked.
Now all that is left for me to do is install the patches anyway as I think their pretty important, hopefully they won't undo the fix or I'll have to uninstall them again I guess.
Tried adding the patches back and it's broken again so guess I'm running without them.
Final Edit: Tried a few times to put the reproccer/skyre patches in but it only broke the helmets again and again so finally I've given up on it. I wasn't using them before and only noticed the helmet issue, so now I've fixed that part I hope I should be ok.
