I don't know why this is some sort of major legal problem. They did some work, not all of it, so you probably owe them some money for what they did. They may be generous and want the car out of their hair and let you take it with no questions asked. Either way, if you don't have the money, don't go poking around stirring things up if everything has been quiet the entire time its been there. Let it stay quiet and go get the car when you have the money. If you can't pay them, don't show up and demand the car back. It doesn't matter if you need the car back or not, they've done work on it so it's their choice whether to release it to you or not without being paid. It's very simple.

If they're happy to store it for you now without working on it, I'm sure they'll be just as happy storing it for you until you have the money you owe them. I don't think they'll put a lien on the car unless the work has been completed and they want the car out of there to make room for paying customers.