once you get rid of the other codes besides code 88 then you can start the timing set procedure. start off by disconnecting the batteries for a minimum of 30 seconds. I would go 5 minutes, then reconnect and only do a key on not start it. check for any codes to see if they come back.
if you have a scribe mark on the IP to move it back to a base starting point, then move it there and just cinch down the top nut to hold the IP. leave the bottom two loose. you can run the engine without the intake installed but I would say install the lower portion so you can use a board or something to kill it in case of a run away condition. make dam sure there is no fuel leaks or any loose things that had the potential to get sucked into the intake.
keep the upper intake nearby to connect the sensors that are on it so not to get any codes for them but far enough out of the way so you can manually kill the engine.
fire it up with the scanner connected and verify no codes still. run it till it's fully warmed up (at least 170 degrees minimum. then proceed with the TDCO procedure. this process can be hell but there is a trick to it. there are two modes for setting TDCO. one is to trigger the time set. then look at the data value "Actual Injection Timing" the reading is in degrees. you want to see 3.0 to 3.5 degrees while idling fully warm. if you see a different reading FULL STOP. shut off the engine and move the IP just a little. (remember moving it 1mm is like changing 3 degrees or so) very fine movements. snug it up and try again. start it up and once fully warm, trigger the set timing. Once you get the actual injection timing as close as possible to 3-3.5 degrees (it will bounce around a little but stay relatively on that number) then trigger the learn on the scanner. that should get you in the ball park. you might see it error out with code 88, but watch the TDCO numbers as it's trying to learn. if you see it stay on a positive number then you can stop and slightly move the IP one direction, too far negative move it the opposite direction very slightly. I forget which way changes the numbers which direction but I know others will help.
Just remember this process is slow, painful, and frustrating at times. just take it slow and with lots of patience.
Oh, and whatever you do, DO NOT MOVE THE IP WITH THE ENGINE RUNNING!!
BTW are you using a tech2 or GMDTscan to do this?