Well, did you over torque the covers? If you did you can check for warpage by holding them against a piece of glass... no biggie. After you reinstall (and put RTV in the right place here too) if you have issues with leakage then you've most likely crushed the rubber seal... and before anyone tried to argue that you can't crush rubber, go look up the shore durometer scale... I'm sick of arguing about stupid shit (not at all directed at you CV).
As for the RTV on the timing plate... you're going to leak oil by the water pump and below the alternator... if it gets bad enough it will soak and ruin the timing belt.
The location where RTV is REQUIRED is shown on these two pages:
(1st picture)
http://www.cygnusx1.net/Supra/Librar...aspx?S=EM&P=55
(1st picture)
http://www.cygnusx1.net/Supra/Librar...aspx?S=EM&P=56
Additionally, there is an order you SHOULD use when installing the valve covers. Tighten the two middle bolts 1/2 the torque value, then tighten the inner bolt toward the front, then the outer bolt toward the rear, then the outer toward the front, then the inner toward the rear... then in the same order torque the rest of the 22 INCH lbs.
I am sorry... I thought you were following the manual with all of this.There are two ways to seal the leak at the timing plate: pull the head or pull the lower timing plate... both entail approximately the same amount of labor, but the head is the one you're familiar with... and the head is the safer bet... downside there is you'll need a new HG. By pulling the timing plate you can slide it off, load in a lot of RTV on ALL of the connecting surfaces and then try to slide it in without pinching the HG thus preventing the timing plate from mounting without a gap... I've done it successfully, but I don't recommend it.
I'll add that I think it's unlikely that ou warped the valve covers... still, you should check them just in case.