Here is the tune file for the truck in question, REP mode.tun.
First off, fix the out of range cells. B6615-B6620 are all out of range when opened. Tunes can do weird things when values are out of range.
P0068 is a rationality test for the ETC that is triggered when the airflow is above what the PCM expects. You shouldnt have to disable the test, but it might work. You've already tried to take the TPS out of the equation, cant hurt to disable this code too. Just be careful, this controls the throttle in case of a runaway situation, if it starts revving with no throttle input shift to N and kill the key.
You are getting P0102 and P0106 because you havent turned off the codes in the Diags section. P0102 is a MAF-related code, I think all of them need to be disabled to really kill the MAF.
Have you adjusted C6102? Might need some work, if the PCM sees more airflow that what it expects it will throw a REP code.
Do you need to adjust C3004 Predicted MAP Min? What about C3906 and C3907, those are TPS related tables.
I have adjusted the DTCs according to the EFILive COS tutorial and fixed the OOR values, it is REP Mode_0001.tun.
What is up with your B3647 Commanded Fuel table? You're commanding 14.7 at ALL RPMS until 95kpa. Probably not a good thing...
Also I just remembered there are ETC tables in the tune that are activated ONLY when you have your FlashScan plugged in. Plug in your V1/V2 and open the tune file. Look under Engine->Electronic Throttle (red folder) at the tables in there. Under the parameters section there are a few cells for idle TPS adjustment... And B2307, B2308 might need to be adjusted to eliminate your REP. Dont know what max TPS should be, but currently it's set at 98.8%, can go to 100% if need be.