The broken USB port issue is a hardware issue acknowledged by Nokia, so if its under warranty they should replace it without problems.

That said, it really depends on where you live. In the US they replaced my N900 without issue (it was overclocked).

Just be very aggressive if they try to deny the warranty (and explain to them that everything else is working), and print out some Nokia emails to prove that it is an issue they are responsible for (Google it).

Good luck!

Edit: Don't even worry about uninstalling the kernel, if they want to check if you replaced the kernel, they can find out even if you uninstall it, AFAIK.