Lexus01,
First, sludge problems are completely related to the lack of oil services. If you have changed the oil/filter at reasonable intervals, I wouldn't worry about it.
Second, If your car is also buring alot of fuel, you may have a faulty mass air flow sensor (air volume sensor in Lexus terms). Not all that uncommon on RX's with some miles on them.
Thirdly, the transaxle is designed to not shift into overdrive until the transaxle fluid has reached 152 degrees. This is to prevent premature wear in the tranny and get the engine up to temperature faster so it meet emissions requirements faster. If this concern is particularly noticeable in colder weather, this may be the problem. Note: please make sure the fluid you used in the tranny is the Toyota T-4 fluid. According to the engineers, the wrong fluid will lead to slippage and possible failure.
The only oddity is the general misfire code(p0330). This could be an entirely different problem, or ist may be related to the dumping of too much fuel into the engine.
Let me know how you make out.
Good Luck
Lexasm