Chris,
A few general thoughts about this problem:
It's important to fix something at the outset and keep it reasonably constant as a reference. What I mean is that it's very possible to get wrapped around the axle trying to vary the thrust profile, while assuming the drag profile to be correct, then finding that it isn't and go around the loop again.
You're probably doing the right thing, but you need to remember that you've a few other parameters to play with - intake area is important for drag at speed, for example, and getting the "dynamic-pressure-limited" top speed at low-level is as important as getting the "Mach-number-limited" top speed at altitude correct: this means paying as much attention to the various drag parameters as to the thrust ones - although the excess thrust at idle is obviously not that!
Lift matters, too - lift-induced drag at low speeds, e.g. landing approach, will make a significant contribution to the thrust required as the speed falls.
Finally, it is well worth taking a good, hard look at the original 'air' and 'aircraft' files to be sure that they are worth modifying, as opposed to starting again with a 'clean' file. Quite often, designers will pinch the basic M$ Learjet 'air' file and then hack about the 'aircraft' file to get something 'fighter-like'. This can take as long to unravel as starting again, so do consider it. Alternatively, take a look at the 'tuning' section of the 'aircraft' file - if you see factors less than 0.7 or more than 1.3, it's a hack - ideally, the numbers should all be 1.0, as everything there can be modified in the 'air file.
I hope that this is of some help - sometimes it's useful to step back from the detail
Cheers,
Kevin