That will be the concern if you shim it too much. Water feed and siphon lines won't seal along with the pump seal.
Yes, I have done the shoe. The hardest part is getting the old shoe off without breaking it as the factory uses a lot of RTV.
The way I did it was to get the alignment tool centered in the through hull fitting and very close to the centerline of the engine PTO by adding shims between the 4 hull studs and the alignment tool. This will set your shims for the shoe. Then reseal/reinstall the shoe with the new shims. Then you can go about final shiming of the engine as normal. THis is how they did it at the factory.