Another option would be to limit the suspension travel - Easily done, find some suitable rubber tubing & cut a piece for each of the damper shafts so that when fitted you can only see say 3-5mm of shiny damper shaft - this will limit how far the dampers can move.
BUT I'm thinking the shell would fit more like the Blitzer beetle though, with the wheels being outboard of the shell, & if there's any clashing of wheels/body, trim the arches so it all clears. ie I was thinking more Beetle buggy than Beetle on-road. If we're looking at going for the on-road look, I'd say there's gonna be some serious (Read un-viable) work needed to get the wheel track reduced to get the wheels under the arches.
As far as unsightly sticky-outy front/rear lumps go, if that turns out to be the case, they could always be disguised with some scale bits & bobs eg spotlights, winch, cargo net, parachute, rocket engines(?!) etc
