Step 1: Make/buy a boost leak tester and see if it has a boost leak, that will 100% cause the symptom you're having (not the codes tho).
Step 2: If fixing the boost leak(s)/none found doesn't fix the issue, watch desired and actual rail pressure to see if it's not building proper pressure. There are many causes for this and we can look at if step 1 doesn't fix the problem.
Isn't the LML the one that's prone to ghost code on delete tunes? I remember reading about it when tuning was new for the LML. Something to do with an unrelated code needing to be disabled that fixed the issue. And not all trucks suffered from the issue. Always results in a limp mode with no codes or DIC warnings.
I think there was two ways to get it out of limp, reflash the ECM, even flashing the same tune will work, or adjusting the offending code and flashing that tune in
You MAY have a bad map or circuit for the MAP. See the attachment. If you have a scan tool, check BARO vs MAP. BARO should remain relatively flat while MAP should change quite a bit if boost actually increases.
I'm thinking that P026D below may be the answer to your problem just because it mentions a few of your codes.
Bd I may have a friend that is a customer of mine that mainly works on powerstrokes that might have the leak down tester but it should work on a lml so I’m gonna see it’s kinda hard when I’m looking and can’t hear anything over the engine