I am curious as to why you cant adjust the valves with the servo motor actuated under idle speed, I dont follow what you typed there??
A way to check and see if the mark is lining up or not is to run the sled on a stand with the servo cover off and rev it up over 7000rpm, the pulley will again cycle to wide open, this will let you know if the mark already there is proper or not. If it doesnt line up the mark either way,below 900rpm or wide open then most likely your mark is in the wrong place. The cdi sends a signal to open and close the servo motr, if you can move the servo further by the wiring harness hook up then with it running you have a faulty cdi box signal, this is common on the 98-99 srx's