Nick - I combines your three topics because you are getting advice in all three, which is too confusing.
In you later pics, it looks like it's time to yank the transom wood straight up sand out. Didn't see any hardware still attached that would stop lifting the wood out.
The splashwell does not need to be removed unless you feel like it. Just make all the screws/bolts through the wood are removed. It is possible the ends of the gunnels need to be bent back for the wood to clear can't tell from your pics.