As the problem which prompted this forum topic appears to be altitude related I would like to suggest you have a look at the Inverse Pressure Altitude (IPA) setting in Records 1503 and 1504 of your .air file before you start messing with drag of any kind.
In FlightSim the Throttle is linked (1503/1504) to CN2 which is linked (1502) to CN1 which is linked to both Thrust (1506) and Mass Flow (1507) and possibly Corrected Fuel Flow. As 1503/1504 is the only link in this chain of events that is altitude related, your problem could be too much CN2 depletion as altitude increases.
This might be the case if the IPA is set too high and the engines might not be achieving the CN2 figure necessary to achieve cruise speed at the cruise throttle setting at high altitudes.
To increase performance at high altitude (without affecting your sea-level performance) you could try decreasing the IPA in Records 1503/1504 of the .air file.
DON'T FORGET to write down the original IPA figure in case you need to go back to it.
As a substantial decrease in IPA may be required to obtain the desired result, if you find you need to reduce the IPA to an altitude below the aircraft's service ceiling/maximum altitude, then you should find another solution to your problem.
In my experience with Jet aircraft in FlightSim, CN2 decreases as altitude increases, and increases as speed increases. It would therefore be reasonable to assume that initial testing/adjusting of this theory for power/speed should be done in level flight at the aircraft's service ceiling.
I used Rick Piper's HS.748 Series 2B as a testbed for the theory.
The HS.748 2B is supposed to have a max cruise speed of 244 Ktas but it was doing 252 Ktas at AUW 45,000 lb in standard Atmosphere and zero wind at its service ceiling of 25,000 feet. Reluctant to mess with the drag settings, I increased the IPA from 4.237 (=just under 35,000 ft) to 5.402485 (=40,000 ft).
In identical conditions after increasing the IPA, airspeed was reduced from 252 Ktas to 246 Ktas and fuel consumption dropped from 1,491 PPH to 1,434 PPH. Increasing the IPA again to 6.242197 (=43,000 ft) should just about get the speed spot on.
If you're presented with several Series of the same aircraft, each with different engine performance, but you're only given one set of engine parameters (as in Rick's 748), the above theory seems to be a simple way of varying engine performance to suit each Series in the set.
There are side-effects to this theory, however (which I haven't fully explored yet).
Depending on whether you increase or decrease the IPA (and by how much), your rate-of-climb/climb-speed will be affected, as will fuel consumption, aircraft attitude, idle thrust at high altitude, rate-of-descent/descent-speed, the time it takes for the aircraft to achieve cruise speed, and possibly Vref/Vat speeds and takeoff run lengths if you're in the habit of popping into and out of places like SEQU and SLLP.
To obtain the altitude equivalent of the IPA in Records 1503/1504, divide (the figure) 1 by the IPA figure in 1503/1504 to obtain the Pressure Ratio, then consult a Standard Altitude Table to obtain the altitude the Pressure Ratio relates to/is closest to.
To obtain the IPA for a particular altitude, divide (the figure) 1 by the Pressure Ratio given in the Standard Altitude Table for that particular altitude.
If you don't have a Standard Altitude Table, I downloaded one from
http://www.Boeing-727.com (Standardaltitude.pdf, single page) which provides Standard Altitude data from 0 ft up to 50,000 ft in 1,000 ft increments.
Hope you find the idea of interest.
Regards
David