Throttlebody Problem, Different Stock Intakes?? Options

[joeladam02]

Two Different Intakes, Throttlebodies...

One for Convertibles, one for Coupes and Liftbacks.

So I put another 5sfe engine in my car and it's running like ****. Garage said there was no vacuum to the Fuel Pressure Regulator, even though the vacuum line was connected from the intake.
So, I thought, pinched line, or clogged tube.
OR
This...
As you can see in the links, there are two different throttle body's listed for the 5sfe motor. One has a third vacuum pipe coming off the top facing the driver's side, and one has the third pipe facing the passenger's side. My original car had the one witgh all three facing the same direction. The new motor I got had the other one. So I swapped back to my old throttle body to keep it consistent with the MAP sensor placement, and other parts on the car. HOWEVER, I did not switch the intake as well.

My question is, does anyone know if these throttle bodies will only work with their respective intakes? Or are they swappable?
This could be my issue, if the gasket is covering a vacuum hole, or if the old throttle body just doesn't line up with the old intake...That could be restricting the vacuum flow to the FPR hose...
I never had the car running with the other throttle body to tell...