Sounds to me like you messed up something while reinstalling the gears.
Personally, I would buy the G-maxx single speed kit and cover plate from Mike and use that tranny.
If you do go with the 3905 tranny, you'll have to also change the center shafts (#1 due to the length difference, #2, It uses Revo style ends). Its definitley a fairly easy conversion, but might be more work than you are looking for. On the plus side, you would get a better slipper system than the 3906 has.
Losi 8T 1.0, Savage Flux - XL style, LST XXL, Muggy, 3.3 E-Revo Conversion and sitting outside 425hp, 831 Tq Dodge Ram Turbo Diesel. It SMOKES
Sounds like the two shims on the output shaft might be in the wrong position... There should be one shim between each pair of output bearings illustrated below.
If you prefer to move on with a new tranny, the G-maxx single speed is a great option.