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Sounds like your clutch needs replaced. Make sure you take the flywheel off and take it to a shop to have it machined. Most likely it's warped which causes bucking.
Your clunk could be coming from the slip yoke on the driveshaft. Take it off and clean and grease it. While you have it off, grab ahold of the pinion yoke for your rear axle. Try to turn it back and forth. Proper backlash for gears are only a few thousandths of an inch, so you should barely be able to wiggle it. If you can rotate it back and forth a bit, then they will need to be shimmed. Gear whine is caused by gears with too little backlash. If your shop adjusts them properly, they won't whine. You may want to find a different shop.
1996 F250, 7.3L, auto trans, 4x4, eclb, TS Performance 6 position chip