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Yes, I'm sure a short block swap would be okay, as long as you can use most of the bolt-on parts from your '07 (intake manifold, water crossover pipes, etc). The '09 has a different EGR setup, and I'm not sure you can use an earlier water crossover pipe. I think the '07 receives EGR from the cylinder head, and the '09 takes it from the exhaust pipe after the front bank catalytic converter. Will you be using the '07 cylinder heads?
 

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It sounds like you're getting the correct engine -- that's good.

The more I think about it, the more I think the 2009 engine *probably* would have worked, though the computer tuning would have been matched to the earlier engine design better. The mechanic would have had to use either the J-pipe or at least the front catalytic converter from a 2009+ model to be able to use the EGR feed pipe. EGR was fed internally prior to the 2009 engine refresh, but this changed in 2009 (in the Ridgeline, anyway) to an external feed pipe. Other than that, everything *probably* would have worked. It would have been a risk, though, and getting the correct engine is the path that offers the best chance of success.

Have the mechanic go ahead and put a new timing belt and water pump on the engine before it goes into the truck, so you have a fresh start on that. Should be very minimal labor with the engine out of the vehicle when he does it. It takes me about 5 hours in the vehicle to do one, but I think it'd be a 1 or 2 hour job at the most if out of the vehicle.
 

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I'm asking out of ignorance, but wouldn't changing the intake manifold still not solve the issue/problem of sensor reporting & engine management (due to different MAP/MAP set up)???
The MAF/MAP sensors are all in the intake stream, so keeping the original manifold and intake system should maintain that system. The MAF sensor is located in the airbox lid over by the fender, and the MAP sensor is located on top of the throttle body. As long as everything upstream of the fuel injector bases (intake manifold, throttle body, air tube, air box) is retained, then it'll continue to operate as a 2006-2008 engine (even though the engine block itself has changed). At least from the MAF/MAP perspective.

Another difference between a MAF/MAP and MAP-only engine is the IAT sensor, or Intake Air Temperature sensor. On a MAP-only engine (like the J35A9), it's mounted in the intake manifold throat just behind the throttle body. An engine with a MAF sensor incorporates the IAT sensor with the MAF sensor. Again, as long as the original intake manifold is retained, that system should continue to work.

My MDX's J35A5 intake manifold, with IAT sensor installed:



My Ridgeline's J35Z5 intake manifold, with no sensor ports:



I think the J35Z5 uses a different valvetrain design than the J35A9 uses. I can only compare my J35Z5 to the J35A5 in our '05 MDX, but I think the A9 in the earlier Ridgeline is nearly identical to the A5. It uses a more traditional arrangement where each exhaust valve has an individual rocker arm, each intake valve has an individual rocker arm, and there's a fifth rocker arm on the intake side that operates against the lost motion spring for high RPM operation. The Z5 uses a different design; each exhaust valve still has an individual rocker arm, but there's a single Y-shaped rocker arm that actuates both intake valves from one cam lobe and a fourth rocker arm operates against the lost motion spring for high RPM operation.

Here's a picture of my Z5's valvetrain:



I say all above that to say that, if there are mechanical differences in newer VTEC valvetrain, there could be electrical differences as well, and some of the solenoid connections could be different.

I think a Z-series engine could be made to work where an A-series once was, but there's certainly less risk in using the correct engine.
 
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