If you do a frame swap you will have to tear the bike apart anyway. That is cheap only if your time is worthless. The real critical piece of information here, which is missing BTW, is money. How much is the lean, how much did you pay for the box of parts and how much did you put into the bike for parts to get it ridable again? If all that adds up to a fair price ($4-$6K), maybe that's the way to go. Pay the lien, and chalk up the high cost to lessons learned. If not maybe a new frame is the solution. If that bike lien is 3 years old and the trail has gone dry the bank wrote off that loss off long ago and they probably have no interest in dealing with you on it.
If you paid that guy with a check for the boxes he is going to tell the bank you have the bike, assuming he didn't steal it or get it from a chop shop. It's pretty likely he isn't the lien holder either and he was just trying to dump it for what he could get. Lawyers cost bucks and any way you look at it you have an uphill legal battle at best.
Just my 2 cents. Hope things work out for you. I know how you can get attached to a bike you spent so much time working on!