I'm not sure if I believe all this magic, but there is something to it. Not much of anything dissolves carbon, and not likely anything as mild as naptha. I mean, have you ever tried to dissolve carbon with anything? You gotta chisel that stuff off... So, let's travel back in time (even older than Beemerdons), when they had water-injection in the old days. Water or high humidity makes an engine run better, and may have kept carbon build-ups down. How? Well water does not dissolve carbon but expands rapidly as it turns to steam. In my younger and perhaps foolish days, an old trick was to mist water into your car's carbeuretor while it was running on fast idle, the theory being that it would flake off the carbon and it would get expelled out the exhaust pipe, albeit with copious amounts of white steam. Quite a sight to see. I never had any ill effects except to stall out the engine if you poured in too much, but always wondered if any carbon was really removed or if a little flake would make it past the exhaust valve before being pounded into the seat as it flew by... who knows, but it never happened to me (I think). Did the car run like magic after that? Not really much difference, as removal of carbon really doesn't do anything, unless of course there was some build-up on the valves.
As for that recommendation in the article to run the snot out of the engine while Seafoam was in the oil, I would highly recommend against that with oil diluted with a solvent.... but another good oil/dirt/sludge cleaner was about 20% auto tranny fluid left in the oil for a couple of hundred miles or so (without running the snot out of the engine, it will circulate just fine at normal revs). More likely that oil additives dissolve stuff better when the engine is at operating temperature for a period of time. It does work to clean dirt out of ticking (stuck) hydraulic lifters, that I know. We don't have hydraulic lifters in FJR's.
Another possibility of poorer performance might be build-up of sludge on the intakes or throttle plates, and sticky intakes can be a source of low compression since they can't seat. We've got a post about that around here somewhere, and I would recommend taking a look before pulling a head off. A leak-down test will tell you intakes or exhaust valves or head gasket.
Ethanol fuels are good at loosening crud and varnish-like build-ups in our tanks naturally caused by gasoline evaporation, but they don't really dissolve it, they deposit it on other stuff, like intakes. Naptha is effective in dissolving this build-up slowly over time, but a big build-up is better dealt with using another method (harsher solvent/carb cleaner) or physical disassembly and cleaning if really bad.
Bottom line, spend some more time finding out what the cause of the low compression is and then plan the method of attack.