I sounds like you've thought this out fairly well, but here's my 2 cents worth from a guy who worked for a non-union airline for 18 months.
JB pay sounds very good for a start up, but still probably 20-30% below current industry standard (we'll see if there will be any givebacks on the new UAL and DAL contracts?). Be careful about hitching your retirement very heavily into a single airline stock (or any single stock for that matter). A lot of people at Enron did that. Also, without a successorship rights in a union contract, if JB is sold, or even if JB buys another airline, you have no legal say on how the seniority list is integrated.
I know many 747 guys at Atlas Air and Polar that were salivating to get on with JB when they first started up, more to get away from Atlas and Polar than anything else, but were very enticed by the new equipment and futuristic thinking of the company.
When Atlas started up in 93, there was no union, pay was pretty good (for a startup), upgrades quick, profit sharing, a matched 401k, and everybody was happy (especially a lot of ex Eastern/Pan Am drivers) to have a job. The company was VERY profitable (generally a 12% after tax profit margin). Schedules were long and tough but the crew force wanted to make it work. There they are 9 years later, pay scales haven't changed, still a 401k, had to sue the company to get their promised profit sharing, reduced benefits, worse schedules (for instance, everybody in MIA is now on 19 days a month reserve), must jumpseat to work vice having the company buy you a ticket, etc, etc. Finally, after the company was the third most profitable airline in the world and no longer considered a startup, the company still refused to raise any payrates AT ALL or reduce the heavy schedules. Consequently, pay "real" pay has actually gone down and, of course, there has been no movement toward industry standard. Schedules are still lousy for everybody, no change in retirement, etc etc. After 3 years of negotiation, their union still does not have their first contract.
Maybe JB can break the typical airline mould of labor relations -- but it hasn't been done yet, at least in the long run -- not even Southwest. Enjoy the ride with JB, but keep you SA up, especially a few years from now.
Good luck.