You don't need an OBD reader, just a paperclip. Check this page out:
http://www.troublecodes.net/ford/
Free & easy. The connectors are between the power distribution block and the blower housing.
You definitely need a pan gasket, just try to find one that's all rubber, not cork or cork/rubber mix. The one I got for mine was a vacuumed to a piece of cardboard with plastic, it had both the filter & gasket. I believe they call it "carded".
Your trans has got to hold more than 3 quarts. I'd bet the torque converter itself holds more than that. I just looked in my Owners Guide (see signature) and the 2 wheel drive holds 9.7 quarts and the 4x4 holds 10 quarts. That's not the pan, that's the whole system. I'd imagine the pan is at LEAST 4-5. Like I said, I had to put in 5-7 just to get mine to engage.
Also, you're not flushing, you're replacing half the fluid. With those miles, I'd recommend getting a in-line filter going for a few hundred miles, especially with the Seafoam knocking crud loose. Then drop the pan and you'll end up replacing half the fluid. This makes it easy on the system.
Torquing is very important. You're connecting a steel pan to an aluminum housing. It's pretty easy to strip threads on aluminum and torquing means you're applying an even force across the entire pan. Doing it hand tight, you might get more tired towards the end and torque them less.