I would bet some cash that is a bearing. They tend to scream after warming up. It doesnt matter if your in gear or not since even in nuetral half of your transmission is turning inside the case anyway. and YES, the bearings are a pain to replace in a regular garage most guys have. The thing is once you're in your transmission and your doing bearings you might as well do a full rebuild. You are going to have to pull gears to get to all of the bearings in there anyway. Chances are once you get your transmission open you wont even be able to tell which bearing it is unless it is getting pretty bad. Order a full rebuild kit and go to town on it, throw away the paper gaskets they give you though. Red RTV is all you need. Another thing is that this is a perfect time to get an AX15. I was patient getting mine and found one after a few weeks of looking for $140 on Craigslist. Will be some of the best money you ever spent.
Complete rebuild axle/engine/everything swap in progress:
Parts already gathered for assembly: 2001 Ford 302, 1990 Mustang GT 5.0 ECU and wiring, NP435, NP205, Pair of axles from 04' F350 SuperDuty (Sterling 10.5 Posi rear, Dana 60HP Front-Both Disk Brakes 3.73 Gears), 37" H1 Tires, 9" lift TJ Coils for 2 link conversion in front, Stage 2 Clutch Kit, 3 Row Aluminum Radiator, Chevy Astro Steering box (4" front Stretch), XJ Rear Leaf Springs (6" Rear Stretch), and lots more.