The bolt heads are gone due to rust, if I just grind them off is there enough clearance to pull the manifold off, then remove the remaining stud? has anyone done this?

 

On the passenger side, that should be doable. Disconnect from the y-pipe, pull it down out of the way, grind the bolt heads off, and slide the manifold off.

 

You could do that if you have either a torch or can let the truck sit with penetrating fluid for a couple days. You should have at least 1/2" after the manifold is off

 

When you say "gone" presumably there's still something to grab on to there? I ask because I just did my exhaust manifold gasket on passenger side a couple weeks ago. I was ready for a fight with the bolts. I let the motor warm up and just to see what I was in for I put a socket on the exhaust bolts and started applying some steady pressure. All of the bolts broke loose with only moderate effort. I certainly could have done it with a pair of vice grips if I was desperate. Didn't even disconnect the y pipe, I just slipped the new gasket in place and bam, runs and sounds great.

Give it a shot first before you grind them off...