Replaced my collapsed lifters with OEM style and the truck never would run right. I am now doing the delete and I have 2 questions.
What do you mean "OEM style"? You replaced the collapsed original AFM lifters with OEM AFM style lifters?
If you haven't started taking it apart yet, can you drive it to your tuner and have them disable AFM in the tune?
1: Do I just leave the sensor on the valley cover unplugged?
As the others said, in the delete, the VLOM will be replaced with a valley cover that will seal off the AFM towers in the block. So, you'll have no place to plug that harness connector in to. Seal off the exposed terminals inside the plug (hot glue in the end would work) and tuck it and/or zip-tie it outta the way.
2: What will happen if I drive it without having it tuned out? I'd need to drive it to the shop as I can't do it at home.
It'll have misfires if it tries to activate AFM. If it isn't disabled in the tune, it'll still be looking for the VLOM. Plug it in and drive in a manner to not let AFM activate- stay in manual mode and 5th or 4th gear if you have a 6-speed. If you have a 4-speed, maybe driving in third would keep it from activating. I don't remember. How far away is your tuner?