Custom proportions causing limbs to twist counter-clockwise

[Misterlegodude]

I'm trying to make a Halo 3 model into a player model without having to re-adjust the model's shape/size, but the pelvic bone and thigh bones are higher than that of an HL2 male citizen, which is why i'm using the proportion hack method to bypass having to re-shape the model to the ValveBiped skeleton

I tried (and am still trying) various adjustments with the positioning and rotation of bones in the model's skeleton, proportion skeleton and reference skeleton, but they only re-positioned that part of the model and rotating them would, of course, [URL="http://i.imgur.com/RdZyp7D.gif"]cause animations to not animate properly[/URL]

I looked through and examined the source files of CaptainBigButt's Miku player model, and seen that the proportion skeleton is mostly similar to the actual model's skeleton, and that the reference skeleton is mostly similar to the female HL2 citizen skeleton, so i did the same thing, except with the male HL2 citizen skeleton as the reference, but the limbs were still rotated 90 degrees counter-clockwise

Then i tried closely following ZeqMacaw's tutorial and the various instructions in CaptainBigButt's 'QC Files' topic, but the limbs are still rotated

If it matters, i'm using the latest versions of Blender, Blender Source Tools, and Crowbar to compile for Garry's Mod/Source SDK Base 2013 MP

And for reference, the highlighted skeleton is the model's skeleton and the proportion skeleton while the black one is the reference/male citizen skeleton
[t]http://i.imgur.com/r3lIERB.png[/t]

The roll values and the head and tail positions of the model's bones are the same as the reference skeleton, except re-positioned to fit the model

And here's the QC and ikchains QCI, the other QCIs don't affect anything so they're probably not worth posting
[url="http://pastebin.com/raw/7r0P4VyM"]ODST_player.qc[/url] [url="http://pastebin.com/raw/TrbhrFRk"]ODST_ikchains.qci[/url]

[B]Edit:[/B]
So apparently i somehow corrected the rotation of the thighs even though i've pretty much ended up in the same scenario as i had previously

I did take yet another different path to get to this one, so i guess i ended up doing something right along the way? I don't even know anymore, but the calves and the arms are still rotated incorrectly and i still can't figure out why