Here is something to check, I was working on an SR25 with what appeared to be the same problem.
If you have some precession measuring tools break them out. Their are some indexes cut into the side of the piston that rides in some grooves casted into the gearbox shell that prevents the piston from spinning inside the cylinder. Sometimes on the lower quality gearbox shells the indexes are either to wide or to narrow. If this is the case then your gearbox gears will all cycle properly when you put the two halves together and your shimming will appear spot on but after you completely re assemble your gear box with spring in place the extra friction created by the piston index will run your battery down and appear as though you need a higher torque motor and gear sets as a result of the spring. This will also cause you to pop fuses because the motor is drawing to much amperage from the electrical system trying to overcome the extra resistance caused by the index.
If this is the problem then it will take some minor modifications to the piston to get proper clearance inside the indexes. After this modification your problem should be fixed assuming this is the problem.
