It's nothing you removed, it's driver and hardware-bios configuration, I'm afraid it would be best first to try without nlite so that we don't put blame where it doesn't belong. You can make bootable iso's with nlite, just select that page, and slipstream service pack too, those operations are safe to not blame nlite if something goes wrong. Well I'm not being defensive it's just it sounds to me that you have basic issues, not component removal related.