Piewagon,
You didn't say if you have a shift kit put in or if you are using a floor shifter. This is a wild guess, but I have seen some wierd things in mechanics. Using a shift kit, the noise could be the hydraulic fluid forcing its way through a passage way when using manual shifting. If you are using a floor shifter, check your linkage, a rod or brace may be scrubbing the drive shaft or universal when the lever is moving during hand shifting and isn't touching when in the drive position. I have rebuilt many th350 trannys and right off the top of my head, I can't think of any internal problem that would act like you describe. I find in mechanics that a good visual inspection uncovers many probable causes.
Truck Tinker
