Nah, it wouldn't be that hard to line up expecially if you used the speaker grill holes to line it up with using pin/dowels and holes drilled through the template and large clamps to hold it in place.
That of course assumes the speaker grill holes are accurately placed from cabinet to cabinet. I'm not sure I would bet the farm on that one.
How did the XO go into this cabinet?
Not too bad. I had to split the crossover into two pieces. One part for the woofer and one part the tweeter so I could get the parts to sit in between the internal braces in the cabinet. When I tried putting them on a single board it was too large to fit where the original crossover was (behind the woofer on the back wall)
Did you upgrade on any of the parts in the XO?
No, I built the base level crossover.
How long did it take you to build the XO?
I built them in a single evening after work. It probably took about 5 hours.