Well, if you are really hitting 38mph on a stock tomos w no porting and just bolt ons thats pretty darn good.
Anyone telling you otherwise is BS, reading their stock speedo, not verifying with a gps or weigh 10 lbs.
Like Gram said put timing where it lets you shift later equalling more power. Do you use a timing gun?Consult timing in wiki. To address the loss of low end torque add a stiffer spring to first gear. I am guessing some has changed out 2nd gear spring already since it shifts at 20 instead of the stock 10 or so.
Are you running an air filter? air filters affect jetting quite a bit on sha carbs, running a stock unmodded box filter changes jetting.
I've had a similar bike a35 sprint with milk crate, black paint, 26/22 gears, opened up stock intake, black cap w two mesh screens, i believe red first and yellow second gear springs, circuit pipe. It was a fun, bike accerated nice, top speed just under 40 is my guess, i weigh 220lbs. A good speed is when my helmet starts to lift from the wind speed hitting my little sun visor and starts lifting the whole helmet up.