So I'm finally swapping out the engine on my 1995 wagon and I'm doing the teardown currently. As I drained my transmission which has been sitting for 6 months or so about 6 qts came out. I thought the capacity for a drain and refill is closer to 2.5 on a 4 banger trans. It also had a lot of crud on the magnet. There was no problem with the trans prior to the timing belt popping so do I just put about the same quantity back or is it time for me to swap transmission too or rebuild this or a spare one

 

I'm hoping this is an AT trans, cause I don't even think an MT can hold 6 quarts.
If it is an older AT trans that has been sitting then it is not unusual for more than the expected 2-2.5 quarts comes out of the drain.
Six I'm fairly sure is the upper total fill of the trans. You cannot get all the fluid out as about 1/2-1 quart is inside the TC and that is about impossible to drain due to its torus shape.
If you got over 5 quarts from the trans when you drained it, then it probably is just from the fluid draining down after sitting for so long. Nothing to be worried about.
On restart dump in 3 quarts and make sure to place the trans in every gear for a few seconds to charge the circuits. Place back into Park, pull dipstick, wipe, reinsert, pull out and check level. Add as needed, shift through gears again, and check dipstick.

 

It's an autotragic. It just seemed lime it had a lot on it. I've never drained this one before.