I'll have to measure them... they were definitely thinner than the dubro wheels... I have those too. When I shimmed the gear forward, I have to grind an angle on the leading gear mounting rails so the retract mechanism would fit in there and sit at an angle. If you haven't done that, that may be part of why your wheels aren't fitting and you're having to block up your retract. I did switch to another set of aluminum wheels, the 4" ESM replacement wheels, but they are fatter than the ones that originally came with my retracts. The ones I'm using now are just about the same as my plastic 4" dubro wheels' thickness. I had similar problems to what you're having until I ground the leading gear mounting rails in the wing. Once I made them angled, things started fitting and working properly.
Holes were just in the top, accidental collision with a dowel rod. I'm thinking about covering it with monokote and painting it.