Looking good, Crazy Cow. I like your plans greatly.
I do have one big objection though, which is making skaven bigger than humans. As-is, skaven slaves are about 10 kilos bigger than a grown man, on average. I've always read that most skaven (especially slaves) are smaller than people. The exceptions to this, to my knowledge) are the Stormvermin and the bigger, meaner leaders (who are likely Stormvermin).
Maybe make slaves around 55000, clanrats at 65000 and stormvermin at 80000? Also, to make assassins better fighters without making them bigger (and unfluffy), you can just give them a higher base skill at combat skills, or better skill learning rates for the same.
To make them faster and more agile, you could put in the appropriate token and give them a more favourable range, so that that too lines up with the fluff.
Also, pop trigger 1 to start sieges would result in steel-wielding skaven laying waste to your colony of some 20-odd dwarves/whatevers before you could ever hope to muster an effective army, so maybe move that to 3 or 4? Just that they use good weapons (read steel) makes them really deadly as a baseline, but showing up early would result in many forts being killed within the first few months, which is likely not great.
Either way, just suggestions, but hopefully valid ones!
As to the Orcs, I personally don't mind female orks, as I know that it is just a temporary hurdle in accurately simulating our greenskins. At the same time, I could see migrants-only as a valid and fluffy way to swell their ranks with only one big intrinsic flaw existing, which is that more fighting = less migrants in DF, but more fighting should equal more migrants (as orks love to go where the best scraps are). So I could foresee there being an anemic ork horde if you are behaving in an orky fashion (as all the death from the fighting would stop the influx of migrants and they can't breed).