That's an odd arrangement, I'm not even sure where to start!  Are the assets being sold to a different buyer than the stock?

Before you approach the tax return you need to figure out the bookkeeping.  Just take it one transaction at a time.

S Corp sells the assets so Cash increases, Fixed Assets decrease and there's a Gain/Loss.  S Corp owner sells shares, this happens outside the corporation so nothing to book there directly (but it will impact the K-1 allocations).  You mentioned loan basis but first we need to know what happened to the note payable between corporation and the selling shareholder.

Sounds like a mess.

Edit: Sorry, started typing before there were any replies and then got sidetracked!