As an idea I would keep the doors as it is , and would use spacers to mount..
if you cut the doors vibration and resonance can increase also..
ps: reason to use large diameter speakers is to have better bass sound that will bring problem inside the door, much better to use the trunk instead I think..
the speakers are not a larger diameter they are still 6 1/2 inch they are however deeper i have already spaced them out but its not enough and i am almost out of room before I hit the door card 
 I am not trying to get more bass out of my front doors i do however want high quality high power handling speakers that dont distort if you feed a reasonable  amount of power  i will run a high pass filter probably around the 80hz mark 
while i am on  the whole idea of a subwoofer is to re-enforce the bass  so you have a full range of frequencys  i dont want THUMP THUMP THUMP i grew out of that almost 20 years ago
In most cars i have heard the sub can be heard working  and you know its in the boot   i dont want sound like that  i want most of the work done by the front speakers and a little re-enforcement of the bottom end by the subwoofer.
ps i have plans to build a transmission line sub cab probably running a single JL 8" or 10"  since i have a large enough boot for it now 

Doug