The angle at the front shaft is already bad to begin with, when you drop the case you are pivoting the motor trans and increasing the already bad angle at the front shaft to make it even worse.
What you should do is leave that alone and have a cv installed or a complete shaft built with a cv.
What is causing the tcase t break, is the shaft bottoming out in it, something is very wrong, t-case don't break like that for no reason.
As for clocking, if you have this angle \ and just move the mounting point of the front shaft lower, you still have this angle \ all you did was move it down, and are still running a increased angle at the front shaft.