Redneck Truck

I believe I figured out the problem with the surging, the lean condition, and the trouble codes.

With the factory A6 computer, the IMT valves operated differently from how they operate now. I'll use "on" to describe when the vacuum valve has power, the vacuum diaphragm is pulled in, and the butterfly valves are pulled away from resting position. Engine speeds approximated.

FACTORY A6:
Engine Off, B1 valve OFF, B2 valve OFF
Startup, both valves ON, and remain on
Idle < X < 3400rpm, B1 valve ON, B2 valve ON
3400rpm < X < 5600rpm, B1 valve OFF, B2 valve ON
5600rpm < x, B1 valve OFF, B2 valve OFF

S6 FLASH:
Engine off, B1 valve OFF, B2 valve OFF
Startup, B1 valve ON then OFF, B2 valve ON remains ON
Idle < x < 5600rpm, B1 valve OFF, B2 valve ON
5600rpm < x, B1 valve OFF, B2 valve OFF

The result is that the engine runs fine from 5600-6500rpm, but has weird surging issues at other times. Because the one valve comes on and back off, I'm wondering if there aren't pinout differences between the two ECUs and maybe the ECU thinks it is operating something else when it's operating the B1 valve. Going to do an output test and see what it shows me. Any thoughts or ideas - maybe a few gurus have seen this a dozen times - please let me know.

Redneck Truck

A little more research:

Stuff appears to be plumbed and wired correctly. An output test yielded the following results:

N156 Intake Manifold Valve operates diaphragm closest to bank 2
N335 Intake Air Switchover Valve operates diaphragm closest to bank 1

Can anyone with a regular 4.2 A6 run the same output test and see what these parts are referring to? I'm trying to find a diagram of when the N335 is supposed to operate, because it doesn't appear to be operating at all, but works fine during the output test.