The clipping problems are probably caused by the bug in the clipnode creation method of XP-Cageys compile tools. Try the various clipnode types and try rebuilding the affected areas, or hope XP-Cagey hunts it down before your map is finished

(which isn't very likely with him recently being employed in the industry and all).
I never use the pitch key to aim my spotlights, so I don't know if it works or not.
To make your spotlights shine the right way, it's probably easiest to just use an info_null to aim the spotlight (won't count towards the entity limit).
Or you can try using the
angle key (in degrees; or -1 for up and -2 for down) or the
angles key (pitch yaw roll) and see if either works for you. You may have to turn off smartedit to add these keys.