Dropping the engine down will solve the clearance issues to firewall which you don't need to modify.. Clearance sounds correct to the rad support panel... Take your exhaust manifolds off and biff them tho as to have the engine in the right place they aint gunna fit. 2UZ Landcruiser manifolds can be used (which also means that the dipstick tube will still fit) but you need to use two bolt flanges and cut and twist the outlet ends in to clear the torsion bars. Expect to spend at least a day on this part.
Hydro fan pump.. As you are going to replace the timing belt and water pump, seals etc (you are aren't you?) pull this off and throw it away. Get the fan idler for the 2UZ 100 series Landcruiser from Toyota which I last priced at $282 plus GST NZD (I was buying them out of Toyota NZ until Toyota Aus began to offer a better price) and the pulley to suit (which Toyota NZ wanted for some reason $220 plus GST yet $78 from Toyota Aus, quite happy to get one for you and post it over). This solves a lot of problems and keeps every part inc belts an over the counter buy. Wiring for that you can either remove or leave in as it ends up going nowhere and can be used for another item (A/C compressor).
Traction control.. Remove the lot.. Drill and tap the sections where the spindles for it's butterfly are to take fittings to connect the IAC valve into and power steer idle up, you'll see why when you get to the air intake but this also keeps things nice and tidy for when it's cert time.
The wiring is going to drive you nuts but it isn't as hard as you think. You match pins and in your case use what is already there in the Surf in terms of circuit opening, EFI, Fuel pump and start relays plus Vehicle speed sensor. It does eat time tho and the hardest part is getting everything thru the original grommet, you tend to understand what the Mrs felt like popping kids out after that bit