I think you got a good deal (and I don't think that's a bad thing). I never did get a complex/HP endorsement while flying the T-34.
If you have a commerical ASEL or commercial AMEL, you do not need a complex endorsement. Those tickets require at least 10 hours of training in a complex aircraft and the checkride has to be in a complex aircraft. So you're covered.
Similarily, an ATP is an instrument ticket. So after you get your ATP, the "instrument airplane" is dropped off the license (assuming you had it). If for some reason you had a non-instrument licesne and took an ATP, you have instrument privileges in the category of aircraft for which your ATP is valid.
A good argument could be made that if your commercial ticket is based on a military competency and that flying was done in a T-34 or T-6, then you don't need a high performance endorsement either. If you go to a FSDO again, you might ask them and if there is any doubt, have the FAA guy throw a one-liner in the back of your log book.
And Gator, if you've lost your civilian logbook, you can get copies of the 8710 form you filled out for the FAA when you got your mil comp done. If you filled in the hours block at the bottom, you can throw those times into a new book. If you have receipts from when you flew or if you flew with someone else that kept a log, you can reconstruct the rest from those. Remember, except for required sign offs or endorsements, a civilian log book is self certifying. It is what you want to put into it. The required sign offs and endorsements aren't needed anymore once the license they were going toward is obtained so if those are lost it is no big deal.
) is supposedly good for the standard Rotorcraft-Helo & ASEL Comm/Inst tickets you are eligible to get out of the HTs. 
