Ok, I went back out and unbolted the cover, looked at everything again, and it was all good. I double-checked that I hooked the lifter this time, and it now works. Guess I'm a little out of practice. It still clunks at idle but once it speeds up a bit it almost stops completely. Its still there though so Im a bit nervous on how long it will last.
She starts and runs but the idle is a bit weird, and when you give it some throttle and let off, it takes a second for it to come back down. I ran through the TPS and ISCV setup again and the ISCV was back to 0.656. So I adjusted it back to 0.698 and reran the setup. And it was back to the mid-0.65s. So it looks like I will be ordering an ISCV, as the WD40 didnt make a difference if it was a bit stuck.
Secondly, I have just read the instructions on checking the secondary TPS and will try it later or tomorrow when I balance the throttle bodies so they are closer together.
Lastly, whatever tune is on the PC5 is now off because it gives a pop on decel. But I dont have the cord and I dont understand the tunes yet so I dont want to jump in and mess something up.