Can anyone upload their txts, if they have fixed this?
I haven't modded my raws for this bug, I just deal with the issue by brining extra animals on embark and culling out sterile females right now.
If you have it, you can use DF hack to fix the orientation flags in real time and get them breeding correctly (There is now a version 40.10 of DFHack, so it's a very workable solution right now). Pretty quick and easy fix when you need to do it. Just pull up the gui on a creature, go to status > current-soul > orientation and set the appropriate interest flags.
For my part, I just embark with 2m2f of whatever domestics I want to breed. That gives around an 87.8% chance of ending up with at least one viable breeding pair. Good enough odds for me. If I really, really need them to breed, I bring 3m3f, and that gives exceptionally good odds for a breeding pair. If a female doesn't breed, either recycle her, or DFHack the appropriate interest.
If you really want to mod all the creatures, you could probably write a quick Python or Bash script to loop through all the txt files looking for the two male/female caste tokens and adding the appropriate orientation tokens under each. Probably only take about an hour or two to write it.
Actually, now that I think about it, it would be next to trivial to do it with notepad++ using extended features. However, it would also mod all the civilized races to get rid of their chance to be gay/uninterested in children/asexual. Though you could go back and manually remove the tokens from the sentient races.
Essentially you do a find and replace in files of:
\t[CASTE:MALE]\r\n
with:
\t[CASTE:MALE]\n\t\t[ORIENTATION:FEMALE:0:0:100]\n\t\t[ORIENTATION:MALE:100:0:0]\n
And the opposite for female. Quick and easy. Just have to go in and manually remove the orientation tags from anyone that you don't want to be 100% heterosexual.