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So I wasn't charting cyst mucous, and I suppose it is possible there were times when I thought I was only dealing with they cyst but it could have masked some cm. Does that make sense?

Yes. You have a bummer of a deal there. CCL will know exactly how to answer this and help you out so that you can minimize your fertile time. I would contact CCL at http://ccli.org/aboutccl/contactus.php. They will help you and their expertise is unsurpassed. The fertile time may not be as long as you would hope but they will give you the longest possible based on your requirements.

Clearly any sex from day 1 to ovulation is out.

This is not necessarily correct. If avoiding pregnancy, you can have sex on any dry day before mucus begins. Unless you are accomplished at telling seminal residue from CM, you should not have sex on consecutive days during phase one. Also, you should be taking internal mucus observations. External can be one day late in showing the presence of mucus.

So, if I were to use NFP again then it's "no, no, no" week after week and then "quick hurry up -now!" one week out of the month if I'm lucky.

I have faced this "lucky" time with my wife. No one has said that NFP is as "free" as contraception chemicals/hormones/barriers. I have thought many times how much easier it would be if everyone of my wife's cycles was the same or if the system was easier or gave us a two day free zone in the middle of the fertile time, etc ... It is rough at times. Sometimes doing what is right leads to frustration. I fail and get ticked too. Things could always be better.

Phase one can be navigated. CCL has for rules that make it 99%+ effective. Three of them are based on your previous cycles. The last is called Dry Days Only. It trumps all the other rules. If there is mucus present, internally or externally, then you are in phase 2.

"Sometimes doing what is right leads to frustration. I fail and get ticked too. Things could always be better."

and that addresses another problem of mine that has nothing to do with charting.

Another freeper pointed out to me how it is tough to consent to something so difficult when you aren't entirely convinced - and I think that's where I'm at.
Because I'm not entirely convinced - and because I'm frustrated and burned out with the whole thing - I'm less inclined to deny sex to my husband 90% of the time.

but thank you for your time and advice.
I will see what they have to say about the cyst situation.