Okay, I'll just post here now that I'm home. There are basically two issues I see that should be addressed. The first one is players who cover two eras. For example, Julio Franco would be in the 1985 draft pool and the 2005 draft pool. I would suggest that if '85 Julio Franco is drafted, then '05 Julio Franco is not available. Also, when the 1982 draft pool of rookies come up (17 seasons after the 1965 draft pool), Julio Franco would not be eligible to be drafted because '02 Julio Franco would still be in the league. Even if he has been cut by the team that had him, only '02 Julio Franco will be eligible to be drafted and not '82 Julio Franco. Not until a player's "clock" runs out (out of eligible WIS seasons) could he potentially be drafted again as a rookie. This applies even if '85 Julio Franco goes undrafted in the initial draft. He still keeps progressing each season. I think that will give the best sense of continuity.
Also, the other thing is the progression of the 2005 player pool. I would say cut those players at either 2009 or 2010. After either 2009 or 2010, those players clocks run out (are eligible to potentially be drafted again as rookies) and the next pool of rookies will be 1885 players (whose clocks have expired).
Those are my suggestions. But I don't care how everything is handled, as long as those things are addressed.