Losi only sell the BK2 wishbones which are identical but have an extra hole out for the VLA on the BK2. So you cannot use that hole with the stock XXCR hubs which the XX4 comes with.
If you tried to use wider driveshafts to make it fit it would no longer fit in the box, so would not be BRCA legal.
I believe you can now use the XXX CR hubs on the X5, but I haven't tried this so have no idea how you fit them.
I have left the extra holes one previously but have heard they can catch on certain types of wheels, not sure which ones. You can of course cut/file/dremmel them off.
Ref the chassis question, you're absolutly right, I forgot about those extra bits. I'd forgot cos everyone does as you have done and just stick a couple of bits of plastic on if you're running the stock hinge pins. If you get some longer pins it should still all fit fine with them left on.
Ref the diff, I assume you are going to run a plastic diff in the back and front then? I can only suggest checking ebay or Losi now do new outdrives with a thin drive ring already on them, I don't use these.
However don't dismiss running the steel diff in the back. I noticed that Tricky and Ellis ( 1 and 2 overall at nationals last year!!!!) both run Steel diffs in the back almost EVERYWHERE. When I noticed this I ran it at Telford national and the 1 time I've run my X5 indoors and am sure I prefer it. They may run it for the binding of the driveshafts against the steel diff, but I prefer the car with a little more weight in the rear, heance I deliberatly run the receiver and transponder at the back, either side behind the rear. Transponder is always a handout one, mounted on its side on a peice of lexan bent into an L shape and taped to the tranny tunnel. Here's a pic of my car from a while back.
HTH
Dan