How can I deal with a short bottom step on a stairwell?
The key is to eliminate any variation over about 1/8" to prevent tripping. You can change the rise gradually and most folks won't notice it.

Sounds like you'll have about a 2" discrepancy to deal with. I'd remove 6-10 treads and start adding wood strips to the stringers to bring the bottom rise to say 7", then add 1/8" to each subsequent rise until you're at 7-1/2". Be sure to account for finished flooring. 

If you want to better handle the tall top rise, remove all treads and work up as I described to its height in 1/8" increments. 

Use construction adhesive and small nails or screws for all strips, and glue and 3" screws for the treads to prevent noise.