Well even after the shift kit i still love to manual shift my TH-350, is their any long term affects from this?

Depends on how the shift kit was installed. If it was setup for manual control then it would depend on how hard you are on the trans (upshifting or downshifting in the wrong RPM's). Definately change the fluid regularly to check the magnet and smell the fluid from the dipstick tube often to smell if its burnt.

If using a good full manual valve body you should have no probs at all as you may have seen from my previous post TH350 or TH400 ? I have run a TH350 manual for many years in a heavily modded Big Block 83 that has run many many low ten sec runs shifting @ 6800 rpm just change fluid and filter regulary HAVE FUN.

Got a th350 in 84 ta and built with shift kit bout 5 yrs ago and do manual and auto shifts with no problems. Change fluid as mentioned earlier. Son says it sounds someone kicked a dog when shifting hard to second.