Ok, a couple of quick things:

As mentioned, the lines go to the fuel cooler. And also as mentioned, someone probably did bypass it due to difficulty/expense of obtaining the correct lines. You might want to look over their handiwork, oft times those who choose this type of repair in order to save a buck or two don't make the best of choices on other repairs.

The A/C compressor is designed to run most all of the time, with the above notations of the Economy mode and the Off position. Otherwise the system operates on the "reheat" theory, where all of the air is cooled and dehumified before being brought to the desired temp.

The color of the caps on the A/C service ports means nothing. They are muck like valve stem caps, and can be obtained in any just about any color or material. Do not rely on them for anything. They indicate neither refrigerant type or pressure (high vs. low). A refrigerant identifier should be used if you have any questions as to what is in the system (it's mandated by law in CA). You should never assume anything, the contents of the system could be R-12, R134a, any number of blends, propane, or air. You should be able to tell by location whether the port is high or low pressure. If you don't know, you should spend a little more time studying refrigeration theory before attemping any D.I.Y. repairs.

Just a few quick notes. Have fun.

MV