Is your block still good? If so if it were me I would take your block and do a fordged 370 stroker kit with a good set of BV heads and a turbo cam so your set to run boost. Now if the 6.1 creat motor your looking at has fordged rods and pistons then yes you can go that way (stock 6.1 only has fordged crank). A 66mm turbo should be more then fine.
This would be my starting advice as well. If your block is good then build from there, however, if you're set on the 6.1 crate engine, then I'd look at at least a set of drop-in pistons to allow you to safely boost higher than 8psi, even if you don't plan to run that high. Since you'd already have the block out of the truck you may as well set it up so you don't need to go back in later.
There shouldn't be any issues with bolt up, just make sure you have the correct reluctor wheel on the crank, there's a 32- and a 58-tooth option and I don't know which an early 3rd gen uses, I believe it's a 32-tooth but don't hold me to that.
You'll also need a different flexplate if it comes with the oem flexplate.
You will need a different intake filter tube, but running a LMI Hammer is the easy way to do it since you can just flip the intake tube around to the passenger side.
I believe you will need to use a truck oil pan and dipstick, the block should have the hole on the driverside for the tube, but the 6.1L pan has the reservoir in the front and it would interfere with the front crossmember.
That's what I can think off off the top of my head. It's all fairly easy to make it fit, just requires a few different parts.