Troubleshooting Head Components

Hey gang, just a thought while the head is being finished. Progress has been slow due to the freeze we had last week. In the meantime, I considered the sludge lingering on the oil pan side of things. Naturally, a change (as mentioned) is in order once the machine is back together. In order to clear out as much muck as possible, would I need to pull the pan and do a good wipedown, then do the old transmission fluid trick? With a squeaky clean head, valves, and all, will the transmission fluid harm or even reverse some of the work done in the shop? I know it won't be clean like a new vehicle because this is a limited rebuild/refurbish, but what other tricks of the trade could cure the chunks floating around? Thanks in advance. I've had a great time learning with you all.