To make the necessary changes, the stock H-pipe was cut in half at the cross-over, and the passenger side was modified as shown above.
Although it now sat closer to the floorpan, the driver-side half of the H-pipe still had plenty of clearance. However, due to the changes in the passenger-side half, it needed to be lengthened 1 inch to bring the crossover back into alignment.
Rather than welding it, the H-pipe crossover was reconnected with a short piece of pipe and exhaust clamps, to ease removal and installation in the future. As wide as the H-pipe is now, it may be necessary to separate or at least loosen the halves to get it in and out.
One of the heater hoses no longer fit, and bending it caused it to fold and kink.
The fix turned out to be as easy as browsing the hose wall at a local parts store until one was found that was a perfect replacement. There is a metal flow restrictor in the stock hose, so be sure to cut it out and slide it into the new hose.
The throttle body now sits almost 2 1/2 inches higher. The initial measurements showing it would clear were correct, but the linkage behind the throttle body had not been accounted for. Removing a section of the underhood bracing gave plenty of clearance.
The new motor looks like a factory install--as it should since almost everything visible was unchanged. The next time the aluminum intake adapters come off, they will be powdercoated black, so it will take a keen eye to notice it isn't just another 4.6 sitting there.