I would take it back the the dealer as long as it's within the warranty window and ask them to correct the issue. First you can try the solution posted in this thread.
https://www.clublexus.com/forums/rx-2nd-gen-2004-2009/752561-cd-player-error-4-a.html
Did you check the level with the car running and warmed up? If so the first thing I would do is a drain and fill of the transmission oil pan with Toyota T-IV.
I would try changing out the solenoid which should not cost that much if you can do it yourself and changing the filter while your in there. With that many miles the only answers that you will get is to rebuild the tranny.
Look up H & R , Eibach or Swift lowering springs for your car. These will lower the car about 1 to 2 inches and give you a stiffer ride. I can't tell you the dimensions of the stock springs.
I have not owned a car with a distributor in a long time but that would not normally be part of the timing belt job. That's more in line with doing a tune up.
Did you make sure that the cam and crank sensors are plugged in? When you say " Does not crank " what do you actually mean? Is the engine turning but just will not start? Lastly are there any codes?
It's flashing because you need to read the AC trouble codes. Check out this thread to show you how to read the codes.
https://us.lexusownersclub.com/forums/topic/3794-ac-codes/
Welcome to the club. First you need to check and make sure the battery is good. If it's good then with that amount of miles it's a good bet that the starter has died.