Underextrusion after long travels
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