Howdy,
OK, so...
>> Before I tried this the electic windows worked fine, now nothing (I can hear a click in the door).
This is probably because the car now thinks that the top is half open, check if you've got a top open light on the dash? This will probably be because of the switch in the top latch if the seller pointed that out, you could try sticking your finger in there (where the lever arm on the latch catches into the hole above the screen) and closing the switch with your finger to see if the light goes out and the windows will work then. The switch in there can go, can replace it pretty easily or just add some padding to the switch as a temp fix so it activates. There's 2 other switches that can tell the car the top is not closed and prevent the windows working, one's on top of the top motor under the clamshell, and one's hidden under the round joint where the top meets the body behind your drivers left shoulder, but we'll assume they are probably ok for now...
>>> I noticed the two cables with ball ends were hanging loose.
Not a biggie, they just put tension on the back of the top and prevent it banging around, won't be part of the issue for now.
So what I'd do next is first check all the major parts and then disconnect them so you can get into that area without breaking anything further...
1) Standing outside the car just to the rear of the door, look down the gap between the car and top and you should be able to see a plastic balljoint on each side, they look like this...
First check they are connected both sides and not cracked. These connect at the balljoint end to the top and at the other end to the transmission, and drive the top movement. If you have the toolkit you should have a long bar like a big screwdriver (if not juse use a big screwdriver). Put this down the gap and lever the balljoints off towards the outside of the car (opposite to shown in the diagram above). with them off on both sides the top should move freely by hand.
2) From inside the car, reach back and unclip the clamshell arms at the pivots so you can open it manually. Look a the thread here,
http://986forum.com/forums/boxster-general-discussions/30176-%2Apop-pop-%2A-went-my-top.html post #11 has picks and post #20 has instructions. With that done you should be able to move the clamshell up and out of the way by hand. The easiest thing to do with it if you're working in this area for a while is unscrew the 4 screws underneath on each side and just remove it from the arms.
At this point you can just screw it all and go with a manual top if you want
But now everything's disconnected and running the motor shouldn't break anything, the next step would be to try unclipping the cables from the motor and slowly running each one to see if you can get the transmission to turn (ie that the boomerang shaped arm that the clamshell and balljoints join on to). If there's no movement on one or both then you'd want to replace it/them. If they appear to turn ok, go through each of the parts in turn and see if you can see anything that looks wrong...
* motor runs, drives cables both sides?
* cables from motor to transmission look ok? (these can be damaged, frayed, particularly the early ones, easy to replace and cheap)
* Transmission turns arm ok? (possible the plastic drives inside have been cracked or just driven past their end positions... if driven you might be able to get them back by running with the drill, if cracked just replace the whole drive with a second hand replacement)
* clamshell arms connected ok, no clips missing etc?
* top pushrod not bent/cracked? (happens, easy to replace)
* pushrod balljoints connected/not cracked? (designed to crack before other more important things break, so happens pretty easy, cheap and easy to replace)
....there's not really a lot of major parts so it's got to be one of them.