Hi Brad,
Been busy at work - Man, would have bet $ that your ride would be on the road by now, sorry its still giving you hell. I wish I could hear the clunk, would help a lot. A couple of places to go - maybe, before it's tear down time: A possability that's easy to check (and therefore discount) Are you SURE it's an engine noise? Under the truck there is an inspection plate on the lower front of the transmission - i think held on with four 7/16 bolts. under that is the torque converter which is fastened to the ring gear (that the starter drives) with more bolts (mine are five 15mm bolts - your's will be different, but they'll be there) check that they are all there and tight. It is possible with extreme caution to run the engine with all of those bolts out and the converter pushed "in" towards the tranny to clear the spinning flexplate, (in order to run the engine while it's disconnected from the trans) but there is very little clearence between the two, and it's probably not in the trans front pump anyway (they usually whine, not clunk) - but checking the bolts is free. Another thought - though never tried it - also free - can you get a small wooden dowel through the plug holes and try to "rock" the piston? Not even sure you'd be able to feel anything, but again, it's free. Worn piston thrust skirts (which stabilize the piston "square" in the bore) will make one hell of a racket if the clearance is too high.
You can also back the nuts off of the rocker studs one at a time to reveal collapsed, etc lifters. There is no harm in doing this with the engine running, but it will get messy. Use a 5/8 sparkplug socket. Back the nut off until the rocker starts to click or clatter. Then slowly tighten until the clatter goes away - this is called "zero lash" now turn the nut 90 degrees tight (1/4 turn) the engine may stumble and run rough -don't worry, it should. in a few seconds it will smooth out again - tighten another 1/4 turn, the same will happen. In the end you will be 1 full turn tight past zero lash. do the rockers one at a time. you MAY catch something as you back each one off - the noise may change or go away.
Gotta go back to work now. Good luck. Jim.