from the reading I had done in the past...the 2.6 G54B engine mounts are the correct ones to use, I didn't know it would be so close to the hood though, our GEN II trucks have plenty of room as the intercooler sits on top of the valve cover. although the JDM GEN I's with the 4D56T had a top-mount intercooler aswell, the specific diesel mounts for the GEN I trucks must be a lot different.

I would just set your hood on top right now before you finish buttoning everything up...just incase you have to pull it out again.