I wrote a blog on handie-talkies and walkie-talkies about a year ago!
There is a rather nice bit of information here as well: http://en.wikipedia.org/wiki/Walkie-talkie
It sounds like you want a walkie-talkie backpack style radio, but a handie-talkie could work as well.
I think it is great you are trying to create a functional unit. The biggest issue is not going to be placing a modern radio inside the box, but alignment issues (as you have mentioned). You also cannot just gut the radio and ditch the stock case. Too bad since that would be the way to go. If the case is made from thin wood, then you could get away with a “dummy” antenna, since the radio may transmit almost as well from inside the wood shell. Do you have a shell designed? It might help to know the interior size constraints (though the original radios are rather large).
Regardless I am sure there are people here how may be interested to see what you come up with.
For a handie-talkie Most of the top-end GMRS radios will work fine, though a few may fit better than others:
http://www.buytwowayradios.com/products/cobra/cobra-cxr925.aspx
http://www.buytwowayradios.com/products/midland/midland-gxt-1000-vp4.aspx
For a walkie-talkie, (depending on your budget) there is also this option programmed as GMRS:
http://www.buytwowayradios.com/products/icom/ic-f6021.aspx
Getting a battery to work with it might be a bit of work though. You could also use a regular GMRS radio, and there are a few that even have a speaker mic: http://www.buytwowayradios.com/products/xlt/speaker-mic-sm300-ml1.aspx