The coolant that you're wondering about looks like "normal" coolant that comes from down low in the block or sometimes the radiator. It's most likely the sludge (for lack of a better term) than settles out of your cooling system. Since it is heavier than the coolant itself, it settles to the lowest parts of the cooling system first. At this point, I would replace the head gaskets unless you have a better reason than this to do so. The solution would be to do a coolant flush after you get the oil cooler back on and the engine's running again. Now is the time to do this since you've already drained the majority of the antifreeze out of you cooling system. You can also install a coolant filter to help keep this build up from happening again, but I would do the coolant flush first. All of this crap will clog your new filter almost instantly if you're trying to flush it through a new filter.
As for the RTV, if there's any way that you can reach something in there and remove it, it would be for the best. While I'm not saying that it will destroy your engine in a few thousand miles if you leave it in there, I'm CERTAINLY not saying it either. There is the possibility of this doing serious damage to your engine. Since the engine's out and the oil pan is off, you should try to remove it for sure. I've seen similar lines of RTV stuck inside oil pump pick up screens. I've also seen them stuck inside of piston cooling jets. If all fails, maybe you could try some mechanical fingers to pick it up, but I'll bet that you can get it out of there.
One more thing to add, if you're thinking about studding the engine, then the head gasket replacement question is kind of a moot point.