quadratec.com sells rebuilt trannys for around $1500. Beefier than stock? If you have a 4cyl, you can swap out the AX5 for an AX15. Unless you are pushing a lot of horsepower, a stock YJ even a 4.0L doesn't need anything beefier than an AX15.
'87 YJ, 4.2L built and bored, 8" of lift, 8.8 rear, AX15/NP 231J, Tom Woods drive shafts, Flat fenders, 12,000LB winch, Custom bumpers, Rattle can paint job. Never completed...