I have only a hand-waving understanding of all the ins and outs of QSBS and it's an area of the tax law that seems to get changed regularly, so I really don't know how to answer you. You do have a "sale" of the stock. that's clear, but the interaction with the QSBS aspect isn't.
It would seem like the first step, though, is to do the lot by lot calculation that's needed and, I guess, if you had a gain in all the lots you could then grind that information through the regular "stock" interview until you encounter the special situations page, and that's where you'd report the basis you've derived and report your gain as allowed by the deal. What's a mystery to me is if you're not able to report your entire gain if the new stock continues to be QSBS, or not, and to what extent.
I just don't have anything I can provide here other than speculation. If you have enough stock to warrant it this might be the time to find a tax lawyer or CPA with extensive experience in this area - I'd think Silicon Valley is loaded with 'em - and let them guide you on this particular part of your income tax return.
