Columbia42-
Well, I can't do much for an autopilot, but I can give you the next best thing: a valid pitch program for the core stage burn, utilizing Altlev's new Universal Autopilot mfd. It's a bit of a hamfisted approach, but I can hit the first stage flight markers (SRB sep, shroud sep, MECO) per NASA publications within about +/- 0.1 km error in altitude.
Only thing is that I was using flight performance estimates from August '08, which had a 329 second MECO. As a result, I reached the 240.8km circular parking orbit at 28.5 inc with approximately 62.2% fuel left in the EDS.
Istochnikov's data was from October '08, and has slightly different flight markers, most relevantly, a MECO of 303.1 seconds at about 7km lower than in my trials. Obviously, the loss of 26 seconds of core stage burn will increase the fuel consumption in EDS, so my numbers, I expect, will drop down to about 50% again. We shall see.
So, back to the drawing board, lol. Once I get the pitch program to put the core stage right down the pipe as currently defined, I'll post my scenario for you to try.
EDIT: An after thought: I may tinker a smidge with your configs for the core and EDS in order to relegate the unused fuel mass as part of the background mass of the vehicle itself. This way, the initial and burnout masses, and the total fuel consumed, will remain accurate, and it'll allow the fuel gauge inside the ship to read 0.0 at MECO. Seems easier than trying to shut her down by hand, and knowing me, if the needle shows anything in the tanks at all, I'll keep going til its gone!