If you put all of those rookies in the farm system what are you going to do about the draft each season? Are you going fictional? If so then why not just run a fictional league form the start? Of course if you do a historical draft then you will have a ton of duplicate players which is a problem. I guess you could do no draft but that isn't much fun.

Plus alot of those guys you have listed as rookies in the farm system were not even drafted in 1987. Heck some of them were still in high school.
Best of luck with this project.