It depends on how bad this bubbling is.If it hasn't broken paint,it doesn't sound too bad yet.It may even be as easy as grinding it down and throwin a little body filler on it or somethin along those lines.But,that dent poses the other problem.

#1 Choice -If your talkin about Jap Patch panels from LMC,then I say no to #1.

#2 Choice-This would probably be cheapest.However,you will be cutting the stuff out at the junkyard,which can be a pain since your limited on tools and space.

#3 Choice-Most likely the most expensive,however you can buy the bed,take it home,and pull the panels off in comfort and with as much room as you need.

Do you have any pics of the bubbling and dents?I think that might help out alot.