<p>I made a print that involves joining two halves together to create the full model. I decided to use hot glue to bond the halves and on one model, the parts came together slightly skewed. Is there any way to ‘unbond’ the hot glue without ruining the model so I can realign the pieces? Touching the glue gun tip to the hot glue wouldn’t work, as the glue is <em>inside</em> the model.</p>

it seems like retraction issue
i would say you should experiment with
retraction length - so it would retract more
extra extrusion after retraction - so the printer could put some material before it will start your next hole :)
unfortunately there is no good guide how much it should retract and how much it should additionally extrude as it depends on "all your printing circumstances" but here is my arbitrary list in order of importance
filament (density - type and producer)
temperature (viscosity - hotter filament flows easier)
nozzle diam (as filament escapes easier through big hole ;)
heat barrier (cooling efficiency - filament should be cool as long as possible up to (or down to) the nozzle)
extruder gearing quality (good coupling makes precise retraction and extra-extrusion)
cooling (fan and duct should cool your printing right after it sticks to the surface)
and one more thing worth to mention
usually the first layer is not cooled which makes whole system hotter (so filament flows easier)
you could experiment with it too especially for big printouts
so
overextrude first layer AND
turn on cooling first layer
it seems like there is a bunch of things you can do to master it :)
good luck - it's definitely manageable