Not cooling properly can be a mixture of things...overcharged, undercharged, improper temperature blend door, yada, yada, yada.
One thing you could check is the compressor mounting bolts as you say the thing vibrates alot, and no you didn't harm the compressor by not having a complete battery load to it. But like I said before...take it somewhere and have someone with the right tools check it out. Usually an A/C to be functioning properly, is supposed to lower the interior temperature or climate of a vehicle by at least 20 degrees from outside ambient temperatures (you can check this yourself if you want). An a/c shop, like I said, will check the charge levels, compare high and low side pressures, and center duct temperatures to a vehicle specific chart to determine if there is proper function and it's simply the a/c not being efficient in the design.