Disconnecting the battery does nothing to fix the problem, It only clears any codes stored in the PCM. The Stock PCM isn't the problem, It works just fine on stock applications, and with a properly functioning MAP clamp and timing controller form Vortech.

 

somewhat self serving input here, but this is where a real Missing Link would solve the problem. It allows the ECU to correct for changes in altitude that voltage clamps cannot solve.

read up on www.synapseengineering.com

 

The Stock PCM has a Baro sensor for altitude correction.

 

what VAFC version?

 

You may be right I was just lending my input as to what corrected the problem for me that's all.

 

Clearing the Code will temporarily make the problem go away. It does nothing to address the issue that is cause the CEL.

 

Correct, but without answers to our questions from the original poster, all we're doing here is swimming in the dark.

 

The baro in the ECU is only used as reference at startup, so you have to turn the car off to reset the reference value. The baro adjustments that the MAP make actually govern A/F ratio.

 

Version 1

Also after driving back at lower altitudes(5,280 ft) for a while the check engine light turns off.

This is what my resident honda expert said "When you are at 0% closed throttle the ECU will blip the idle air controller for a split second and look for a change on the MAP sensor voltage. SInce your Black box and VAFC are heavily modifying that voltage the ECU probably cant see it. Then it sets a CEL for Map sensor. I have seen this on a few OBD-II cars with VAFCs and high altitude driving. (above 10k feet)
"

 

What are your VAFC settings?

The only time that the VAFC is modifying voltage is when you have told it to do so. If you're not making any adjustments at 0% then the "blip" should not matter. In addition, if the ECU is "bliping" you should have this problem all of the time, not just at high altitudes.

Have you had the VAFC tuned?

I'd say pull the VAFC.