Fritz,
ChkMods should have put IL2.exe in there, but it did not. My bad. I left it out somehow...
I do not think with modding like you did removed the il2.exe, I'm pretty sure it was not there from the start.
What I meant by my sentence "(And, for sure, that's not the case after using ChkMods.)" is that I knew for sure ChkMods would leave you with an IL2.exe and an IL2fb.exe which are not identical.
In the end, that was not true, due to mistake I made. So basically, ignore that one sentence...
Did some googling on the Stab thing, check these threads on the issue:
http://simhq.com/forum/ubbthreads.php/topics/3226041/all/IL_2_Shturmovik_Stab_6_3_help.html
If you now have both an il2.exe and an il2fb.exe that are equal, then ... I do not know what is wrong with ILStab, why it won't run...