1. Take the carb off. It's only 4 nuts and disconnecting some linkage and vacuum hoses.
2. The FSM says to loosely bolt up the manifold assembly to the head and check for any gaps. If there are none you don't need to machine anything. I didn't have to and mine seals fine.
3. Always tighten the bolts up that hold the manifolds to the head first, then tighten the bolts between the manifolds.
3. Also check the hole where the hot air diverter flapper thingy goes through the casting and make sure you're not leaking too much there.
4. Did your desmog eliminate the EGR cooler? Check to make sure your EGR block-off plate isn't leaking if so.
5. Exhaust dump location sounds pretty good, shouldn't be having problems there.
Start reading at this post for a very detailed picture description of how to install the manifolds:
Rising Sun Bio
2F "Brahma" + Lockright, tach, Warn 8274, FJ60 Power Steering,
no more Sanden OBA
1FZ-FE factory lockers +
Safari intercooled turbo, CDL switch, cup holder, Metric TLC leather, heated seats, JDM switches, PUMA OBA.
Warn M12000 waiting for a bumper.
Limited TRD 2UZ-FE SOLD