If the hammer is too badly out of alignment you can remove it, heat it with a torch and bend it slightly to bring it into better side to side alignnment with the nipple.

Base pins should not be a bear to remove and install but should not be loose, such that they fall out by themselves, especially under recoil. Remember that they are not the same length, there is a front and a rear. One trick if they are too loose is to bend them slightly. If they are extremely tight, figure out where they are tight and relieve that area on the gun gently. Mine go in and I have to push them the last 1/16 with my ball starter. I use my ball starter to get them out by an initial push in the other direction.

That clean out is for cleaning the entry hole into the patent breech. Since to get into that passage via the nipple would require a flexible claning tool it is easier to remove that set screw. Remove it now and add some never-sieze ot the threads.

as for barrel cleaning... how far from bottom does the jag come from touching? It should go to the bottom of the barrel / breech plug with no issue. I will use a bronze brush from time to time to clean the square bottom rifling followed by patches. some warm water and some dawn to clean it out. I always remove the nipple before cleaning...