yes maybe if you want to change some parameters its cool, but try to draw the extruder itself it would be a pain in the a#* ...
Changing your told values would only take about 10 minuts with sketchup (even with importing the stl again)
why do you want to remove the nut holes ? wanna make life more difficult ? ^^"
there is a reason for the holes also have an offset, thats not just for fun.
check out the prusa xcarriage i
made, without them it would be very difficult to assembly all parts.