John,
It's a known problem. If you can work out how to get the gear into Van's holes you are better than the rest of us (slow or quickbuild). Start with the holes he draws for you as a starting point. (Just trace the template onto the fuse in upside down position and cut).
You will have to make the hole progressively larger as you go. One of the nutplates on the top of the spar may need to come out for clearance (the outboard most one).
Do not worry in this area you will install an intersection fairing over the hole some minor irregularities in the hole can be accepted. Van wants you to seal up any gap with fuel tank sealer or RTV.
Also, another tip. Watch out for the rivet on the lower longeron that will get in the way of the weldment pushing right back onto the spar. Van has you set five of the floor rivets double flush but it isn't too clear on the plans that there is one 1/8 rivet on the lower longeron that needs the same treatment. I just modified the weldment a little to clear.
This process takes some time... but it is not a difficult job.
Good Luck!
Richard