Thanks for the reply... After what I went through yesterday, and now your post, seems I've bitten off more than I can chew. I'm fairly mechanically inclined, but this task seems a bit over my abilities. I really don't want to damage the engine getting something wrong. I had to go down attempting this repair because a repair shop (now 1400 miles away from me.) did my valve check and CCT replacement and botched putting the oil cover on correctly. They incorrectly installed where the two long bolts should go, one being at the top of the cover. This bolt resides right over where the cam chain runs. Putting the shorter, incorrect bolt in this location caused the threads to fail and they got sucked up into the tensioner blade, damaging it. I tried for weeks to get local shops to do this repair, but kept getting turned away. My situation might require a call to Yamaha for assistance finding a repair shop.
I will give you answers to some of the questions you've posed... I have a manual CCT installed and it is fully retracted - no factor impeding the chain. I took pictures of the cams before I removed the intake cam for reference. One of the problems I have (and I think you echoed this) is when I begin tightening down the cam, per the process in both the factory and aftermarket repair manuals I have, the intake timing mark moves out of its desired location (by about a tooth). I have also tried to put the chain on with the bearing covers removed, but his still didn't offer much help. Initially, I had the chain tie wrapped on the exhaust cam, but this only further impeded the chain clearance issue. And yes you are right, I found slack at the crank sprocket. I removed the sensor, but do not want to risk moving the crank by taking anything else off. I might try one more stab at getting everything back together, but I'm very apprehensive, as I don't want to damage the engine. Again, thanks for your insight and experience regarding the quandary I've gotten myself into...