I have not had your problem, but I have a 97 boxster. In late 98 they came out with an upgraded set of cables for the top that had reinforcement in the plastic sheathing. This kept the plastic from stretching when very hot (summer heat and engine heat did it).
The problem was that the cable inside the sheath did not stretch and this caused it to become disengaged from either the transmission or the motor. That's where the popping sound comes from.
I'd say you could save a bundle on parts for this repair, but you live in Beaverton where Sunset Imports is located and they will not give you good prices because you're not out of state. I could buy the same parts from Sunset for a LOT less.
Be thankful that the left or the right side of the top didn't keep going and cause the whole top frame and the painted clamshell to become bent. If you think your top repair bill is high now, you'd have been totally freaked out by a $2500 repair bill.
You should buy a Bentley repair manual for your car and study all the pictures of the car even if you never plan to work on it. It will really help you learn all about the car and why it does what it does when it breaks down on you. My wife always teases me for this consistent "bedtime reading" I do because I pour over the repairs and pictures and then take it to Hans to have it fixed... but I'm becoming very knowledgeable about my car!
I do find it odd that BOTH transmissions need to be replaced. I'd ask them to show you WHY they both needed to be replaced before they install new ones. If they can't prove to you why they don't work or the cable receiver is stripped out, they're ripping you off for a couple of cheap cables ($24 each plus installation and top timing reset).