Lexus Repair: 99 RX300 computer issue, fuse box, reputable shop

Question
Hi. I have a 1999 RX300. This summer the transmission was slipping. A very reputable shop here in NC rebuilt it.  The same thing happened again.  They put in another rebuilt trans. from another 99 rx300.  It did the same thing. Finally, the shop owner researched his magazines and found an article siting the computer as the cause - not the transmission.  (said it doesn't tell the transmission when to change gears properly)  The article said to "flash" the computer.  He did.  Thankfully that fixed the transmission slipping.  Now, just a couple of months after the whole 6 week ordeal.... the transmission is hesitating - just a little - again.
Now... it mainly does it when you first start the car in the morning.  Also, occasionally the control panel for the radio and air won't work.  If you turn the car off and back on it fixes it.  Again - mostly on a cold start.
The combination of the two - and the fact that the car runs perfect 99% of the time leads me to believe that there is a problem with the computer / electronics.
Additionally, to me at least, it is like the old days when you would have a crack in the distributor and a car would malfunction if it was cold or wet. ?
I know this sounds strange, but I'm wondering if there could be a short in the wiring (though why would the transmission mainly hesitate in the morning) or maybe even an issue with the fuse box and the power it supplies?
Are you familiar with this problem?  Any info you can offer would be greatly appreciated.  I would like to know who to troubleshoot this - and if it is going to be very costly.  I really would like to keep this car.
Thank you!

Answer
Hello Clark,
 As far as I'm aware there are no reflash for this year and model. When R&R you will have to reset the ECU by using a Lexus scanner. Back to the main topic,  How do we know for sure the valeboy and the transmission itselft wasn't put back together properly? What are the line pressure?  Any CEL?  Have your guy take a look at the TPS(throttle position sensor).  It's located back of the throttle body.  We ran into problem a couple of times. The dash light is a separate problem that you are having.  The screen on these do go out. Also it wouldn't hurt to check your battery voltage and alternator output. I would bring the vehicle to  Lexus Independent shop an have them take a look.   Thank you.
 JP Importz
DAllas Independent Lexus & Toyota Service and repair