You can try using ASIO 4 ALL or whatever it's called - a decent ASIO driver that will work with most cards.
If you want to record more inputs, just get a decent interface.
If the guitarist played a few different parts to the click, and they were all in time, but he couldn't get one part in time, it's him not the computer. If EVERYTHING is out of time by the same amount, then it's latency.
You can set cubase to play a click, create a new audio track and set the audio source in your PC as the "what u hear" thing, record the click track, and play it back with the midi click at the same time. If they're not in time, then you have a letency problem!