Pull the lines. Have a bowl or something to catch any fluid that drips out.
If it's a separate cooler, clean it out and you can use it for power steering fluid or engine oil - the units are similar.
Or, if it's a separate cooler and you don't want to use it for anything, flush it out and give it to someone for the shipping (I could use one - hint, hint.)
If it's the integral cooler, pull the lines, flush it out, and forget about it. You won't lose any coolant - if you do, you have bigger problems to deal with.
I tend to use radiators for automatics whenever I do a swap, since they're designed to throw off more heat (needs the extra capacity for the tranmission fluid circuit.) Keep it - it will work better.
Now, if I can only find a decent, cheap little MJ... I need a small pickup!
5-90