If you plan on adding these hacks back to your forum after you upgrade to 3.5 then I would not go the impex route. Just upgrade the forum as you normally would (upload new files, run upgrade scripts) then start re-applying modifications after you've done that.
This way all your custom info will already be in the database, and you can use it instead of bringing it over by hand. Going the impex route is going to mean more work for you. The php modifications will be gone when you upload the new files, and they shouldn't care about the custom tables/colums you've added to the database.
Always back-up and do your upgrade on a test forum first.