Pretty much depending on the year of manufacture, the keyboards/pedal board may be wired either parallel or matrix. This in part would determine which encoder. Parallel being one wire for each key (note plus a common) while matrix uses fewer wires with the addition of matrix diodes. An easy way to check this is by counting the (approx) number of wires coming out the wiring harness(es) of the manuals and pedal board. Depending on the number of manuals you wish to convert will also determine which is the best/better encoder to be used.
If, as you say, the electronics are flaky, I would eliminate all of the boards involved and basically start from scratch. Sometimes a flaky (intermittent condition) can be traced to one or more "cold solder" joints. If you use boards or connections where this condition was present in the past, you'll continue to have the problem(s) in the future with Hauptwerk organs as well.
Quite a while ago, before Hauptwerk, I repaired an organ by re-soldering every connecting point. Took 2 days. Never did find the exact point of the original issue, but the re-solder did the job albeit a long one.
Rgds,
Ed