The Intake Manifold Tuning (IMT) system could be source of problem. It modifies air flow based on engine throttle/load. Blocking the extra port may affect how this system works.

Suggest checking STFT at various throttle positions looking for excessive leaning (+STFT) or enrichment (-STFT) at higher RPM's. If present, IMT system may be blocked or not performing as intended. You may need to return to OEM configuration (matching upper and lower intake manifold) to cure your problems.

good luck

 

Thanks Tex, I did check STFT and it got up to around -25% at 3500 RPM, but when the misfire kicked in both banks dropped to 0%. I can go ahead and swap the intake when I do the valve adjustment, but It doesn't have the Bypass valve actuator (or the bypass valve). Would I just leave this disconnected?

Does anyone know what engine uses an intake without the bypass valve system?

EDIT - Did you mean I should try to swap the Lower intake manifold? I so, I unfortunately returned that with my core engine, just kept the other upper. I could probably source a lower manifold if needs be though.

 

Yes, I did mean to match upper and lower intake manifolds.

regards

 

Alright, I'll take some time to sort out the intake situation and do a valve adjustment to be safe.

I suspect it would be best to replace the lower manifold to match the the upper from the original motor so it uses the bypass valve correctly. Do you think its worth trying the other upper manifold and not using the bypass valve system at all?

For reference - 17150-RCA-A01 Bypass Valve Actuator Assy. | ACCORD ACCORD HYBRID Honda Part

The bypass valve is part 8 and connects to the flapper valve. Both the components are not included in the intake that came with the new motor.

 

Abrupt change in STFT at rpm where IMT is likely to open suggest IMT is likely source of your problem. You could try disabling the IMT to see if it makes a difference. If yes, then more proof of IMT problem. This is likely to set a code.

Going to original equipment arrangement is best bet to a fix.

good luck

 

Alright, I'll see what I can come up with for a new lower manifold set. In the meantime, how would I disable the IMT? Just disconnect the Bypass Valve electrical connection?

 

Yes, unplug connector to IMT motor.

good luck

 

Latest update.
I pulled off the valve covers and upper intake today and did the valve adjustment. I have not reassembled yet. A few of the valves were outside tolerance, but none were seriously so (only 2 didn't fit the feeler gauge, the others were either fine, or just slightly loose or snug). I'm not sure how far out of adjustment they would need to be to cause runtime issues.

As far as the intake - I did finally find a thread about motor swaps, and its just the difference between a manual and automatic transmissions, so swapping the intake shouldn't be the issue. After I got back in there I realized I'd also swapped the lower intakes, so that all matches up. Disconnecting the IMT didn't make much difference, if anything, it was slightly worse.

Here are the two upper intakes from the bottom:
Automatic Upper Intake:
Manual Upper Intake:


Before I reassemble - is there any thing else I should check out?

One other side note - in this picture you can see two coolant lines I capped off just below the intake, since they weren't on the other motor. Does anyone with an automatic know where these lead? Can I loop them together? The caps don't seem to be holding up.
Looking at this photo they both go to the AT, so should be ok to loop.

Lastly, the front and rear banks under the valve covers were significantly different colors (Front was very dark, rear was golden) - is that normal?
Rear:
Front:

EDIT - if photos don't work, you should be able to see them from this link in an album: https://goo.gl/photos/GiRsggDV1tnLixDL9

 

The coolant lines should connect to the two nipples on the throttle body.

Color of valve trains looks fine to me. No crusty carbon build up. Difference in color not obvious in photos.

Make sure gasket between upper and lower intake manifolds is good.

good luck

 

Update:
Problem is multiple misfire and exhaust rattle over 3500 RPM under load, if held at or above that RPM for 15-30 seconds it sets codes P0300-P0306 (all the misfire codes) Misfire doesn't occur when parked and revving through the range.

So far I have:
Adjusted the valves - No Change
Swapped the coils (1 at a time) - No Change
Cleaned the EGR - No change
Checked Short Term Fuel TrimsChecked Manifold PressureCleaned spark plugs - No change
Compression Check - Disabled IMT - No change - maybe slightly worse.

Only things left I can think of:
Spark plug failing under load
TPS/MAF/MAP/02 Sensor (no codes for these though)
Catalytic Converter
Fuel Delivery/Low pressure

It's simple enough to swap some plugs. Any tips for checking the fuel pressure? I have a gauge, but there is no tap, so something would have to be rigged.

How about checking the 3 cats?