Is there a way to get the roof into service mode from the down position with the deck latched in place?? I can't figure out how to get the deck unlatched..? Any info would be awesome!

Also, is there a way to close the roof in an emergency when it's not working like this and its locked in the down position? We were wanting to take it away this weekend on a 6 hour drive, but I'm concerned if it rains...... lol And when we park it at night it would be nice to put the roof up... any thoughts/suggestions??

I also can't get the windows to go up, so I guess that would pose my 3rd question - will the windows go up if I can get the top up? Or am I looking at multiple problems? Or?

I'm curious as well. They left everything disconnected, but with the top up. They left it this way so they don't have to undo everything again when the motor comes in.
They left all the covers and parts in the rear trunk. I also found the new relay in there. When they tried it and it didn't do the trick they put it back in the box and left in on the service counter.
I don't think I should pay for the relay as it's not in the car. I'll find out in a couple of days.
When their "diagnosis" of a bad relay didn't work, I suggested the motor. They said they would try that first. It didn't take too long to get the call at work that the motor was dead. So does that mean I found the problem. I told them about this forum and renntech. They didn't seem to impressed though. Probably since it causes them money in service diagnosis.

Flyride, I'm new to the forum as well, and to this problem.
In my research I've found several threads at Renntech.org that tells how to put the top in service mode. I believe it's also in the owner's manual, haven't checked it lately.
Once you have released the black and red (may be white) ball joints you should be able to move the top (Tool Pants explains it the best over at Renntech).

As for the windows, it could be a microswitch either at the top latch or on top of the top motor.
When the top is not latched and not in the full down position (you don't mention if the top light is still on) the windows will go down but will not go back up.
What I found works to check on a microswitch is to remove the top relay. This will bypass the latch microswitch and allow you to raise the windows. When you replace the relay, the windows should go down about 3". If you can't bring them back up again, then the microswitch that tells the relay that the top is fully down is not sending the right signal (either B pillar or motor microswitch).
(Search for microswitch or relay on Renntech) also use the microswitch trouble guide in this thread:
http://www.renntech.org/forums/index.php?showtopic=5208&hl=microswitch