"Common Denominator" was a freestyle. That wouldn't have been on the album. It came out a long time before 1999 too.
"Night Shift" and "The Settlement" definitely were supposed to be there but were cut. The "Night Shift" beat was really good and was later reused for 9th Prince I think. I don't know why, but Loud maybe wanted to try something more commercial with him (they were about to go under around that time) and they put wack shit like "Forget Me Not" on there.
Deck is an example of a missed opportunity. If you listen to him on Liquid Swords you start to think of what might have been. I wish all members could have gotten the full RZA treatment like Meth, Dirty, Rae, Ghost & GZA did. I mean, come on. How else is U-God gonna make anything worth checking?