Everyone of your problems is caused by the base-coat and nothing else.
First these problems will always show up first in Dark green, Dark blue or black colors as they are about twice as slow to dry as most colors. A few reds, like guards-red will fall in this category also but only a few.
*Either you are using a crappy system. (low grade)
*Using improper grade reducer for base-coat.
*Not letting base flash long enough between coats or before clearing.
Take you pick, its one of the three, how to test the theory? Let one of the bases set over night before clearing, that will compensate for a lot of errors.
All your problems are solvent related to base, contraction and traped solvent deep down, that is why sometimes it takes two weeks to show up, usually in first coat of base.