I'm not sure why your deck lid didn't lift high enough for the roof to go into the trunk. The roof should not have even lifted off the body unless the trunk lid was open all the way and the switch closed to allow power to go to the roof. With out seeing what you have going on I can only guess as to what may be wrong but you should be able to get the roof to complete the cycle if you have a second person to lift up on the rear deck so there is enough clearance for the roof to clear the deck lid. If for some reason it won't lift high enough you can either jumper the deck motor either at the motor it self or by the solenoid behind the rear seat, or you can take the pins out of the deck lid lift jacks and then you can lift it even higher.
The deck lid is counter balance with springs so it is not heavy if you take the pins out, you could operated the top with the switch as long as you have a second person to control the deck lid.
I hope this helps I wouldn't waste my time with a mechanic unless he actually has worked on a Skyliner before, if you buy the top manual you should be able to fix it yourself. If you are unable to work on the top yourself be prepared to spend a lot of money because most top problems take a lot of testing to figure out and if you are paying a mechanic $100 or more an hour you can get a big bill fast.