I would like to be able to seamlessly move a site once it is up and working...

If moving an ez publish website to another webserver would create permissions problems. How difficult would it be fixing the permissions (are there a google of them?, are they hidden and deep rooted?, etc...).
I'd recommend installing a fresh copy on your web server, get that working properly, the copy over the design changes you made on your local copy, rather than the entire application. You should find that all your changes are within their own directories and can be easily moved.

The problem with ftping the whole of eZ publish is there are alot of files which may need a permissions update. I've never been through that.

I've read in some forums (here and elsewhere) that eZ publish is too resource demanding and too slow to be run on most shared server accounts. I've just installed it on a dedicated server and it runs ok, but what would happen if I had (and I will have) to run it from a shared server? Will the slowdown be unbearable? Will the ISP kick me out of the server?
I've run it on a shared server and the speed was acceptable. eZ publish 2.x isn't particularily fast it's true, although is being significantly improved in version 3.x.

Suggest try it and see - for testing it's not going to upset your ISP. It really depends on how many people share the server.