The reservoir for the power steering needs to be lowered, but that is all that is generally known to be an issue.
What motor mounts are you running? Was this a converted 6-cylinder frame?
The idler on the bottom of the passenger side should be really close to the crossmember. Some people have gone to the extreme mounts to raise the engine a little, or shim the motor mount, or even notch the crossmember. I believe there are 2 different diameters of that pulley as well, one clears better then the other. In short, the pulley should be really close to the frame. How much clearance do you have?
No reason it can't fit under a stock hood. It has been done before. Without a body lift.