It was decided that the best thing to do for the cost, was to swap the valves with the T-valve retrofit kit (Pentair 230067), which includes a new drive train, base plate, and the 5 replacement flapper valves (along with glue and the other necessary parts). The swap converts the older style valve, which uses balls, over to the newer flapper style, which is probably more reliable (and definitely smoother operating).
The pool valve in question, has had a bit of a rough life, with several cracks sealed up using JB weld (some of which had to be ground away to fit the new valves), and had some rough looking valve seats. The valve had been run for a time without the balls, which I suspect may have caused some of those issues with the worn seats.
The T-valve conversion went OK, however the instructions kind'a suck. Most of it is pretty obvious, but there are two things which stood out, the first is that they provide a small block (which is a chunk of plexiglass) to serve as a spacer tool used to help install the valves. I used that tool (according to the instructions), but when I watched videos on how the pros do it, they did not use it (and I think I see why after the glue had set lol). The tool seemed to create a bit of a less ideal alignment due to the worn valves. I think if the valve seats were not as worn, it would be less of an issue, so I won't suggest one way or the other on using that "tool" or not, just that it did not work great in this case. The second issue was that the instructions (as far as I could see) did not mention where to locate the cam plate when installing the gear train for the valves. I had to watch a video to find out where it went (turns out it is 180° from the hole in the base plate). It was where I thought it should go based on the indents in the base plate, but it should have been spelled out in the "instructions". Maybe it's just some secret handshake stuff they don't want their customers to know about :D The instructions should have included at least one more pic of how the final assembly goes together, but instead they included one which seemed pretty obvious instead. A side note on that linked video, he installed two washers before the impeller, but my kit only had one (and the original had only one washer).
Prior to installing the valves, I noted that the seats were worn, and mentioned that, but didn't want to press the point (turns out I should have, since it would have saved a bit of work). When I installed the valves I found that some of them seated with the frames appearing a bit off from where I thought they should go, but since the valve seat is the primary concern I went with what felt right when the valves were "seated". As I half expected though, the heads did not cycle properly after the swap, and it was clear water was bypassing though some of the failing valve seats. I decided I would try and repair them with some epoxy putty. I'm no pool expert, so I expect I didn't pick the best possible stuff, but I used some JB Weld "Water Weld" putty, to repair the valve seats. The alternative is to replace the whole valve housing, which requires a good deal of excavation and pipe work, and expense for new parts, which is not in the cards right now.
Since the valves were glued in already, using the putty to repair the seats was a bit of a pain (but also somewhat helpful). I first scuffed things up a bit and cleaned them with alcohol, and then pressed the epoxy putty into the valve seats. I had to mold the putty to the valve openings with my fingers, but due to the tight spaces, that was a best effort deal. Some plastic pry tools with thin flat ends helped to get the epoxy pressed in at the back of the valves where my fingers could not really reach. Once I'd made a sufficient mess of things with the epoxy putty, I put some silicone grease on the valves and pressed them down into the valve seats (which had a bit of epoxy putty on them). I'm not really recommending this process, but just to be thorough, I have to emphasize that it was important to keep the silicone grease from contaminating the epoxy as I went, so I went though many pairs of rubber gloves as I had to work one valve at a time. The grease was only applied after the epoxy had been laid down, and used as a release agent on the valve seats, to keep the epoxy from sticking to them during the process. I did have to press the valves into the putty a couple times, to make sure the epoxy layer was pressed evenly, and was thin enough. With the valves pressed down I also removed some of the excess epoxy around the valves. Then I carefully lifted the valves back up, and used some silicone grease on a q-tip to clean any epoxy off the valves themselves, and let things dry that way (with the valves flipped up). After a day of drying, I gave things a quick check and lightly sanded any areas that felt too much out of place, and retested the valves. Fortunately the seats appeared fine, and there was no interference with the movement of the valves or the cam.
After that it was just buttoning up the whole valve, with the steel shims, the rod post, the cam (which is opposite the hole in the base plate), the gear train, the all important washer, and then the impeller gear. It seems to be working well, but time will tell if this repair will last. I've been surprised with the prior leak fixes using JB Weld on this same valve, which have lasted for years now.
Unfortunately I found that one of the pop up heads is now sticky, which had been a preexisting condition, possibly related to running the heads wide open for months while the valve had been free flowing. That is a small problem though, and the pop-ups are a cheap and easy fix.

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