The best thing you can do for the ATX tranny besides driving conservatively is to maintain it. Maintenance is just doing a full tranny fluid change every 50k or more, dropping the pan to replace the filter and clean the pan, with a full torque converter flush where you disconnect a front cooler hose and run six quarts of new tranny fluid through with the engine running (the first few quarts of flush can be a cheaper fluid if you were going to blow $120 on redline synthetic for your fillup). Then regularly check the fluid level the correct way - a full warmup drive, shift the car into reverse, drive, and park, and then check the level with the engine still running. The level shouldn't change, so you will catch a leak early. Keep the fluid level at the top mark.
When you do the transmission swap, I would replace all the transmission cooler hoses and completely flush or replace the cooler too, so if the old transmission spit out metal shavings, you don't contaminate the new transmission with that junk. The torque converter is not the first thing to fail in the ATX, so I wouldn't worry about replacing one with just 60k on it.
If you don't know the full history of the 60k transmission, you also might consider having the bad one rebuilt. A wrecking yard transmission can be a gamble.