Heres a couple things:

1) how tight do u tighten the trans case screws? You want to slide them through the case, then put a dab of blue locktight on the ends and tighten them down on the motor plate then back them off. I also put a ballstud washer on the opposite side where the screw head is so it evens out the preasure on the case..

2) Check you motor plate they tend to bend causing misalignment.

3) You said u replaced all the gears except the topshaft? Even though it looks good by eye that also can bend slightly cause alot of noise, and stress. Specially on the trans bearings, idler gear, and trans case.. Not to mention spur gear wobble..

4) Check the top shaft teeth make sure there nice striaght and clean, also the other plastic gears 1 little piece of debre can cause i chip on any of the gears and will make noise..

5) how fresh arethe bearings?

6) if u can find the older plastic idler and diff gear the white ones they seem to be a little softer and mold better to break in...

7) A BIG thing to check is the spacer that goes inbetween the end of the topshaft and bearing in the trans.. Some had to make it a tad bit smaller in overal size by putting it flat against a dremal cutting wheel so it takes a even amount of material away.

8) When i build a new trans or replace gears i always break them in before running on the track for best effecincy.. (THIS SEEMS LIKE ALOT OF UNNESSACARY WORK BUT I GUESS ITS JUST A OLD TC3 HABBIT) this is what i do 1) i build the diff no special way,2) then i build up the trans like the instructions say..3) i put a dab of this paste i have it has grit in it i forget its name but some use to use toothpaste..4) mount a old stock motor in it with a big pinion. 5) then hook it up to one of my chargers that has a motor feature and let it run for like 5-10 min on a low voltage like 3 volts.. so it wears in the plastic.. 6) disassemble the whole thing rebuild the diff so its race ready, clean all the bearings really good, reoil them, clean all the gears with a tooth bruch so they look brand new.. 7) then i always use a dry lube.. i only put a dab or 2 on the idler gear making sure it doesnt contaminate the diff...8) then i reassemble like normal... never had a prob with noisy trans( knock on wood)..
But like i said it makes the trans very eff.. and it will have no drag and spin forever and last forever..

Like i said it just my habbit and im sure many will disagree but thats what i do