Jeeze. I've been wanting to reply to this for two days but it took me this long to get enough time to read the whole thing so I don't ask something someone else has already asked (and had answered) 973 times.
Anyway, before I heard anything bad about the 3650 I picked one up on Ebay to go with a 5.4L DOHC swap into my 96 GT - first major mod I've ever done to my car (or ANY car, really). I haven't really experienced the grinding issue, despite this being a used transmission of somewhat unknown vintage (I was told 4k miles but now that he has his money the seller won't respond to my emails, so I'm hoping he wasn't just making up stuff). I DO have an issue that was mentioned a couple of times in this thread, though, which no one has yet responded to.
At idle the car is NOISY. It sounds like the transmission is full of rocks or something. It shifts pretty well, though I've noticed (as others have commented) that it gets pretty notchy after getting nice and warm. It seems to like being driven hard - the best shifts are always the ones when I'm beating on it a bit. The FEEL is no worse than my old T45. The T5 I had in my '88 coupe with 5.0L was smoother, but it had a Pro 5.0 the whole time I had the car, so it's really not a good basis for comparison.
To give a bit more info:
In neutral with the clutch released, I hear a sound like a random rattling - no real high- pitched noises - not like metal contacting metal - it sounds like a rock polishing machine with a full barrel. Almost like a REALLY bad throwout bearing. The noise goes away completely when I press in the clutch and all I can hear then is the exhaust. I do have some other minor stuff - if I listen closely I can hear some gear whine when accelerating in 3rd and possibly 4th, but those don't seem like too big a deal.
I don't recall the name of the 2 other people who mentioned this same issue, but hopefully they're still around and will chime in.
The cost of the swap has pretty much wiped out any money I had for diagnosis or repair for quite a while - so I'm hoping someone here can give me a clue about what to expect here, without me having to have someone tear the tranny apart and see what's wrong. I don't know what's "normal" for these things, and I've never had a brand new car, so I might have more trouble than I think simply due to being unfamiliar with how good it's SUPPOSED to be. It certainly doesn't shift "like butter" as some have said their transmissions did after the Ford fixes.
Any thoughts?