I know this is an old thread, but did you ever find the problem? I am realizing a similar problem... After pulling the engine twice, I'm thinking that I have a wrong timing chain... It seems that 1999 is a split year and there are 2 different timing chains... I will know more by tomorrow... It seems that GM decided to go "unconventional" and changed whatever setup they had and went like 6 degrees off on late 99 and 00 engines... Then the 454 was cut altogether and then they came out with the 8.1L which has a different timing chain setup, yet similar to the earlier 96-98, and early 99... Even the 502 crate engines have a similar timing chain to the 96-98 and early 99... I have a used 502 crate motor cam, but I didn't know the year, but I am feeling that it's a late 99 or 2000, in which GM must have manufactured the cam on the same basis as the production cams... The chains themselves are the same, but the late 99's use an S830T cam gear and a S815 crank gear... Hope that helps and hopefully this will work!
Mike