Thanks for the replies!
I do have a 1" body lift, so over-the-top is not out of the question. I was concerned about being able to make the tight bend right after the header with 2.25" pipe. Also, I'm worried about the heat buildup at the back of the block; I've heard that's why 3VZ headgaskets blow so fast. If I drop down, the clearance between the front driveshaft and the bell looks tight.
I'll look at crossing over further back, but I am also running an auto, and I think the tranny cooler gets in the way.
And no, I don't have smog to contend with. So long as I have a cat and no CEL I think I can get it through.