You didn't tell us how much running time you have on it since last cleaned. If you have a lot of time on it, I would consider this normal for using 5/29 fuel.
Changing to 10/11/11 fuel would minimize this.
Crock pot cleaning using antifreeze is the least damaging, or least potentially damaging way to clean things. You already have it apart, so do it now.
I would not use steel wool on any of the parts. Shouldn't be necessary, and getting strands lost inside the engine if you don't get the parts clean is not going to improve the run....
The antifreeze will remove carbon buildup, but may take a few days. The worst I've seen were a set of Fox engines I rebuilt for a guy we can call Al Carbone. I cooked those guys for at least three or four days but they all came out clean. If your liner is still black after the carbon comes off, that suggests it is a temperature-induced discoloration. That's a different deal, and you're going to put the parts back together, regardless. Just for info, if the color change is truly "black," that indicates a temperature somewhere around 550F to 600F. I would expect the combustion chamber temp (at the top, near the head) can get into the mid-five hundreds, so that is not proof of overheating to me. The fact that the liner "fell out" suggests that the heat transfer from the chamber walls to the case is poor, meaning that the liner will get hotter and discolor more than one with what I would call a proper fit. I am not a fan of dressing the bore of the case so that the liner floats, for just this reason. Other guys insist that they relieve the case bore to keep from distorting the liner and screwing up the running fits. My preference is to find parts that are actually well machined, straight, cylindrical, etc. so that "rework" to loosen the fit is not needed. This brings me to a related point...
If it ran really good before on 5/29 fuel, and there is a loose liner-to-case fit, I would be very careful about going down in oil content or substituting to a high percentage of synthetic oil. The concern being that you are likely running the liner hot, and doing anything that allows that temp to go higher is not going to be helpful. Better to run a hundred flights with a castor-heavy mix and then dunk the entire assembled engine in the crock pot. Also, letting the crud build up on the outside of the engine is another way to cause heat to build up. After each session, spray it off with cleaner.
I wouldn't worry about having to "break the engine in again" if it is properly reassembled. If the parts are good, there's no reason it shouldn't go back together and run the same. If you have trouble getting it to run the same, then either your methods are not proper, or the parts fit was not good to begin with. Top of the list for improper methods would be damage to the liner trying to get it out. Since this one "fell out" inadvertently, I suspect that means it was not grabbed with the nearest pair of pliers. Next, if the engine is assembled with crud under a sleeve flange or in the head land and the screws torqued down, causing things to warp. Next, the ring is somehow abused trying to either get it off, get it on, or simply get it back into the sleeve. Don't take the ring off! Or, if your engine has ball bearings, all kinds of ways to snarf that up by improper disassembly/reassembly. The outcome is all some variation of "it doesn't run like it used to."
Good luck with your engine. Hpoe you get it back together and running as well as it used to,
Dave