youre going to hate this reply but here it goes

if in deed that is a 99-00 motor just sell it. its not a good motor to work with. the internals are junk, the crank is longer then others. its agood block to make a good 408 from.

that motor will never work with that tranny unless you swap out the crank. top if off the rods of that year motor are really weak compared to othe LQ4s