Here's a pic of the engine compartment with all of the issues numbered.

1. The auxiliary air Line is missing. Ron you noticed this in my other post so I'm assuming from your original comment about the car running rough on a cold start that replacing this line will fix the problem? I'm not sure how long the PO had it off. Would it have done any damage to the air flow system? And does anyone know what size/type of hose it needs to be replaced with?
2. The Water Hose from the engine to the controlled-by-pass thermostat (which looks like its missing also) is capped off. Is this bad? Should I replace the thermostat and the hoses?
3. I'm not entirely sure what this vacuum line is for? Its a clear hose that is also capped off. While the engine is running you can see the hose sucking air. Anyone know what its for?
4. Any ideas what this plugs into?
5. Just thought I'd show this one before someone commented on whether or not the brakes worked, they do, but not as good as they probably should. The brake reservoir must of cracked so the PO decided to putty it closed and only use half of it. There's only one line coming out of the reservoir then its been split with a "Y" connector into the master cylinder. I plan on replacing the reservoir with a new one. Does anyone know what size/type tubing comes from the reservoir to the master cylinder?
6. I'm assuming this is a sensor or some kind of control for the cooling system. Its still plugged in but the wire coming out of it has been cut. Is this a critical piece of equipment?
Thanks in advance for helping out this newbie mechanic.
Rick