I recently was forced to replace the engine in my '98 Camry (5SFE) myself, and, wonder of wonders, got it working with the help of some family members over the course of about three months worth of weekends (to my own continual amazement; I'm not a mechanic by any stretch of the imagination. Also: DEAR GOD THOSE THINGS ARE HEAVY.)
So it's been back in service as wife's daily driver for about a week now, and anytime I drive it, it's with the windows down and the radio and air off so I can listen for potential problem noises... I'm pretty paranoid about that now. Here's what I'm hearing:
Anytime the car is in a forward gear and under load - not coasting or idling, but accelerating - I hear what sounds like a faint high-pitched metal rasping sound in addition to the engine purr. The sound was such that at first I thought maybe the brake pads were worn, but it goes away if I'm coasting. It's most noticable during acceleration from a stop (heavy load on the transaxle). It's also tough to isolate because it only happens under these conditions; if I just park it and pop the hood and stick my head in there, it's not happening. Also, when you can hear it, the pitch seems to follow the engine RPMs.
Prior to changing out the engine, there were no known issues with the transmission. The ATF was topped off afterwards with a Dextron III "equivalent" (a ton fell out when we pulled the transaxle off the motor and, not knowing what we were doing, the torque converter off the transaxle) but it wasn't flushed, and it still shifts smoothly and normally. I'm now seeing that
the differential has it's own oil fill and drain caps, and wondering if any of that could have leaked out as well and if I'm driving on a dry differential, which kind of freaks me out.
As a side note, I believe the ATF is overfilled. It's a good inch or two over the "Hot" notch on the stick while it's warm.

This... wasn't done by me. I, uh... wasn't sure how to read it at the time. I've read that overfull ATF won't cause windage or foaming like engine oil, but still, should I drain some ASAP or can it go until the weekend when I get it to somewhere with proper tools and space to work? I've been
told that this isn't a likely cause.
Wife drives with the windows up and radio and baby both talking at once, and so has never heard it. You can really only get a good listen when you're driving with the windows down next to a truck, van, wall or hedge or something that reflects your sounds back. By the time you get around 45MPH the road and wind noise drowns it out.
I also thought water pump, because the radiator keeps sucking the reservoir dry (hopefully now fixed) and I have an occasionally squeaky belt (residual from power steering fluid leak, now fixed, I'm hoping that's all it is now), but I replaced that pump with the engine, and I'd be able to hear that while parked and listening under the hood.
I also thought wheel or CV bearings, but it doesn't seem to follow that pattern and turning doesn't exacerbate it.
So... am I just being paranoid and hearing things I wasn't before? Are there things I should immediately do to avert a catastrophe? This is the regular standard automatic transaxle on a 5SFE. (Sure NOW he tells us!

) The transaxle is original equipment, and was swapped to the new engine.
Thanks guys, great forum.