1998 Chevy Tahoe

Ok, first-- a whinning fuel pump is normal. The fuel pumps are naturally loud in these Tahoes. Check the fuel pressure. It should be around 66psi. If it's not, change the fuel filter. Check the fuel pressure again. If it's still low, then and only then it may need to be replaced. A word of caution though, changing these fuel pumps usually opens up a bad can of worms.
Second-- what name brand parts did you use when you tuned it up? What did you do when you did the tune up?
Third-- The clunking at your differential could be a few things. Check the U-Joints first. Then check the differential yoke for any play, especialy up and down. The front pinion bearing commonly fails. Any type of problem with the U-Joints or the pinion bearings can easily lead to mis-diagnosis of an engine hesitation or problem as such.
Fourth-- If the transmission fluid and filter have never been changed, then it's probably time for new fluid and a new filter. If the trans. Is not slipping or anything, then the problem you suspect may be something else. Check and fix any or all of the preceeding before blaming the transmission.

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