DTCs affecting tune

[NJ_Phil]

So I finally convince the wife to drive the car and that it's a "normal" car, just like when we bought it. She's was scared to drive it after seeing it ripped apart and sitting in the passenger seat after a few burnouts. She drives it, check engine light comes on and and it goes into limp mode in the middle of rush hour traffic and we have to push the car into a parking lot. She swears she'll never drive it again, ugh.

Turns out I've been tuning VE with P0106 and other DTCs detected by the ECM which explains my weird VE map. The 0106 was caused by the 3 bar map sensor and luckily I had my scanner with me, cleared the codes and back to normal. I'm confused by how the DTCs are handled and reported by the ECM and what affect, if any, they have on the tune. I understand the SES warning can be disabled with the checkbox, but is that disabling the error or just the displayed "Service Engine Soon". Same for the MIL and why have the ability to MIL of 1st or 2nd error? What makes it a "2nd" error?, 2 days in a row, 2 consecutive engine starts, ???

Understanding the DTC is easy, I just don't understand the MIL on 1st, 2nd, Ignore DTC and Enable SES checkboxes and can't find an explaination on how these affect the car.
Also, which DTCs affect the tune or performance. I don't want to just disable them but don't want the MIL light on either.

Right now I ignored P0101, 0102, 0103, 0106 just to get me going but sure that's not the right thing to do.

[schpenxel]

Enable SES check box doesn't really make any difference to the ECM, it's just whether the light turns on or not so that one is pretty simple. ECM behaves the same regardless of this.

I've never been clear on what the computer actually does after the first time an error happens on something that is set to report after 2nd error though. i.e. does the MAF fail if frequency is too high/low once, or does it keep using it anyways and wait for it to happen again? Seems to me it would make more sense to stop using it then monitor it to see if it happens again or not. I'm curious the real answer on this too--I know people say you have to set the MAF fail to first error, but do you really? I haven't tested it to see.

The only ones you really should need to disable are rear O2 codes, maybe a few others as they pop up but there's not much. Some shops will disable tons of them but I've never seen a need to.

101 and 106 you can disable, 102 and 103 are probably MAF failed, either on purpose or otherwise

There's a section in the engine diag-->airflow tab where you can disable the test for 101, 106 and 121.

[NJ_Phil]

Possibly the 106 error switched fueling to the MAF table which isn't tuned yet or just dumped 20% more fuel in as a safety. I had disabled the MIL indicator for 106 and didn't see it so tried to tune around it which put it in limp mode.
I know the 106 DTC alters fueling because I was looking at LTFTs and they went from 1% to 20% exactly when the MIL light came on when I re-enabled 106 to MIL on 1st. Good thing I realized that or I would have started increasing airflow again. LOL
Regardless, it's disabled now, DTCs are cleared and I'm back at square 1 tuning VE.