The task isn't impossible but can be difficult if you're trying to merge the two separate sites into one instance of DNN. FYI, You can run separate instances of DNN on the same server.

As for doing the actual moves....it's going to take testing, retesting, and more testing. A lot has to do with the modules you're using on the sites and whether they support the Export/Import feature. You also have to get your users moved over (there are a couple of modules on Snowcovered that do it well).

Here's how I'd initally plan to do it:

1. Wipe out the current install of DNN on the new server including the database and copy the 4.3 site over to the new server and restore the database. Do not make it live yet just use this as our test base for now (I usually setup a test sub-domain in IIS and edit the portalalias table to point to it).
2. Once I know my test site is working I'd do the same thing with the 3.5 site but on another test sub-domain.
3. Once the 3.5 site is up and running I'd do the upgrade to 4.3 (something that I don't think is in the documentation but is a good idea is to delete all the .vb files in the DNN 3 site before upgrading).
4. Now you've got two sites running 4.3 and this is where it all comes down to how well everything imports and exports and could (probably will) require a lot of sql commands to get the two database merged into one.