Still Eligible?

Yes, the clock was running. This happened to a friend of mine, left an NCAA D1 college after his frosh year, worked for a few years, wound up going to an NAIA school and was the 1st pick of the Buffalo Bills.

Krakatoa -

The only way to make sure of course is to contact the NCAA and have them rule on the specific circumstances. My understanding is he is no longer eligible. The clock started the first season of play and the 5 years can only be extended if the circumstances are "no fault of the player" i.e possible medical red shirt which can extend play to 6 years in some cases. If baseball stopped because the player voluntarily left school the clock kept ticking.

Krak,
The 5 calendar year rule only would apply if he enters a D1 school next fall. He could instead enroll at a D2, D3, or NAIA school, and have 2 seasons of eligibility and 6 full-time semesters left in which to play.

Except for D1, eligibility doesn't expire until the player has been enrolled in 10 full-time semesters (or 15 quarters) or has completed 4 seasons of competition. Presumably he's only used 4 full-time semesters.

For NAIA, eligibility also expires when the player graduates.