Found my leak, the sight tube was leaking so I addressed that. The clear tubing that was used was not good enough at high temperatures so it got hard and brittle. I extended the sight tube away from the water jacket by 4" with some pipe nipples. And then also used silicone tubing which should be much more heat resistant.
Then i found the real leak. On top of the baffle near the back was a rusted spot that was just dripping but once I cleaned it up with a wire brush I found one tiny hole and one about 1/4" and an area that was about 1"x6" that was rusted down pretty thin. It looks like it started at least 1/4" thick steel. It had no cover on the chimney when I bought the house so it was getting water in the top and this is right where it would puddle.
First I tried high temp JB weld that comes in a little jar that says good to 2400F. It said cures in 2-4 hours at room temperature. So I wire brushed it clean, wiped it down with brake cleaner and then smeared it on. It is more of a paste which worked well and didn't drip through the holes. I kept it warm for 4 hours until it felt hard and then refilled the boiler. At first it held but within minutes it was leaking bad.

I kept the fire going to get some heat back in the house and let it go out by next morning. Once I got in there I discovered that the stuff "unset" I don't know what to call it. It turned right back to the paste it started as and wiped right off. So I cleaned it all off and used some original JB weld which says it's good to 550F and being on the water jacket up high I doubt it will get that hot, it does not face the flames. Of course that drips through holes so i used some coated screws with a washer type head stuck through the two holes and then covered them with more. I spread a decent layer in the rusted thin area. And then kept it around 80F with a space heater for 24 hours. I'm past 24 hours now but I won't fill it and start it until this evening after work.
I'm sure others have done this. Will it hold? The only way to access for welding a new piece in would be to first cut a hole in the bottom of the baffle, or possible to take the roof apart and cut the chimney off and reach down from the top and then reweld the chimney on after. Picture shows an arrow to where the leak was.