I've been exactly where you are as my truck had a very deep thuinking sound after it was rebuilt. You can follow along with my nightmare here by my message #148631 - August 10, 2007 . It was the crankshaft that didn't get enough oil and I had to pull and rebuild the motor a second time. I'm no expert but I recommend you stop driving it until you can determine what is making the noise. Drop the oil pan and look for metal filings. I found alot in mine. It ran great until it warmed up and started thunking... good luck.
