1st major mod... what would you do?

The most glaring problem with Crusty is the tranny will be 1st thing to get repaired/replaced. While I would rather spend time and money else where, if it is gonna get me around it will need to attended to shortly. Instead of rebuilding the unit I have, I would prefer to buy and build a second one and keep my core as a back up. Let me state that currently the stock one is ok, out of o.d. and as long as you have some throttle to it, otherwise shudders.I work less than 5 miles from home and put probably less than 200 miles on it total a week and mostly between 30 and 45 mph. Anyway, back to the question... I wanna build a frim drivetrain to handle later improvements. If you were gonna build an od tranny for a wagon how would you do it? This is a "family" car that will never see the strip or road course, will go long distance, maybe tow light loads (atv's ect) and likes to stab the gas to scare the rice kids.
I plan some decent mods...upping the cid to a 350, retaining the tbi, adding a emc, larger injectors and pump... I should be able to modestly pick up 100 hp or more.
What trans would you build? What parts, ratios, convertor? What would you use and why? I am totaly open...suggestions?