I wouldn't dare let any chemical stronger than store bought degreaser come near the engine. The guys that completely restore rare motorcycle engines take apart the crank cases, set the gears aside, remove the o-rings and bead blast the engine cases to a smooth finish. Then they paint or polish them. The o-ring kits are really cheap and can be found on Ebay easily. If you have it taken apart this far you might as well replace the 40 yr old seals! I have shown how to do it here on the forums so it shouldn't be hard for anyone else to do so.
The only machine that I used for cleaning engine parts was a transmission cleaner that only uses really hot water. This I used for the cylinder heads because it blasts water between the air cooling fins really well and cleaned it right up. I think every professional transmission shop in the US has these cleaners and you can put the engine in one of these as well. Asking the guys nicely and handing them $20 for beer should get your engine cleaned up really fast and you wouldn't have to leave your engine there or wait more than 15 minutes. Of course if you already have the cylinder off you should put it back on so the water or any cleaners don't get inside.
But the rubber seals are already worn out so don't worry about hurting them. You can re-use them and if you use your Honda it will just get dirty from the oil residue slowly coming out over time.
Now the cylinder is iron so you can't hurt it with chemicals. But I still wouldn't put it in a chemical tank for radiators or whatever. If it's a nice expensive harmonic tank with agitating agents then yeah, I'm sure you'll be fine. If there is paint on it that you want to get off they sell aircraft stripper that takes the paint right off. They sell it in a steel can and they sell it in the aerosol spray can (super dangerous if it sprays on you or splashed back!). But be super careful as you need to wear long rubber gloves and eye protection and a hat FOR SURE. That stuff will sting the moment it hits your skin. But the paint will fall off after contact with the stripper for 1 minute. Then you just brush it off and then use water to rinse when your done. I've used a lot of this stuff and it works the best. But the transmission washer should get all the dirt off that you need the best.
To clean the bottom end out while the cylinder is off I would spray WD-40 in through the cylinder base to rinse anything out and then drain through the oil plug. It it has any dry dirt or cobwebs in it I would put a cup of solvent in and shake it then drain. THEN quickly use some WD-40 to rinse and coat everything. Then when you put it together and run it make sure and drain the oil after the first half-hour of operation. This would make well and sure that the inside is flushed out and the new oil would be clean. The oil we have today is far better than what they had when those bikes were in use. Just use regular 30 or 10-40 and you won't have a problem at all. Synthetics are just not needed and cause early leaking in older engines (especially if the old oil seals are re-used!).
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