I checked our manual and some of the old tech support newsletters they put out--it's too bad they're not online anymore--but I'd still say to send them an email or call for tech support. Everytime we've dealt with them, before & after PSI had them, they were really helpful. They pretty much say to clean the tanks out by running several cycles of warm water through them. There are some tips for combatting algae/scum growth in certain tanks, but it seems flusing them out with water is their first suggestion.
We've done this, so that's why I mentioned it.....you pretty much fill them up with water & instead of setting up the trough with dam & spacer and all that--you run it through it's cycle & pump the water out through the trough drain. You run the level all the way up to max, and each time the process goes to a new step, you hit "step" to skip over the wash cycles or to move through the tanks to go back & strat over again. It's kind of a pain, and can take awhile...there's also a way to disconnect those heaters & such (you have to go into the back of the machine-- into the guts), but you need to be really careful not to pump the tanks dry or below that bottom line. Don't overfill either. I've siphoned chemistry out of them too, but this is a real PIA and you need to be careful of the heater probes etc. The thing to remember is that the machine is always on. It sits there 24/7 ready to process. So you can't really turn it on to mess around with it without having it hooked up or parts of it disconnected.
.fwiw, I don't think you'll ever get them totally cleaned. It might not matter if they're stained really--as long as the crap doesn't contaminate the fresh solution or come off and get pumped into the trough, you'll probably be okay. Processors get really nasty after a couple of years in use, they never look as good as they do brand new.
Sorry--I've only done E6 in them, so I can't be of much help on the b&w...we do b&w in a deeptank with TMAX RS, but I don't think that would be too hot (would be hot actually) in a WL, unless you could slow it down somehow by dilution or messing with the pH. There is a small processor called a Super Sidekick--Phototherm makes these--you could see what they recommend. XTOL might be a good one too, it's just that it's going to be continuously agitated, and the tanks themsleves are large--so you can't fill them up with something that's going to go bad quickly--the nitrogen will keep the solutions good, but eventually they crap out--you need to plan on trying to use them ASAP or using at least a gallon or so a week, so you can "top off" the tanks with fresh chemsitry.
I guess it would depend on what temp the tanks are set at and time you feel comfortable with though. I guess you got the right tube sets, trough dam, process cards etc.?? Do you have a water panel yet? The machine has a backup battery that probably needs to be checked out, and those tank seals need to be changed periodically along with the trough dam--these rubber parts crap out and cause leaks and oxidation problems. The only other thing I can think of offhand is that for b&w, I guess theoretically if the ambient room temp were too high, you might need a water chiller or the cooling exchange units they make to hold the temps down low enough. This isn't a problem of course with C41...
they're great machines though, so good luck with it.