As for the difference in dimensions between the .30-06 and the 9.3X62, I know that folks have been using the '06 case (or now, probably the .35 Whelen) to form 9.2X62 for a long time. In fact, I have a couple of Speer manuals which recommend that. Also, remember that the body of the 9.3X62 is longer than the body of the '06 which gives the Euro/African favorite a bit of an edge in powder capacity. No, it's not a bean field rifle, but all in all, it's a pretty neat and efficient cartridge for those who want a lot of thump at routine game getting ranges. Sounds to me like a neat project.
I have a VZ24 action I'm saving for a project that, like you, leaves me debating between the Whelen, the .338-06 or the good old 9.3X62. Personally, I think any of the three would fill a wonderful niche for climbing around in the black timber after elk or slogging through wet thickets after moose or even hunting black bears over bait. (There I go, day dreaming again). And yeah, they would certainly handle whitetails, too.