I found it interesting reading the posts from people saying "he's a roofer, not a swamp cooler installer." I think this illustrates the differences in the way things are done in different parts of the country. I'll bet those posters live in the east where you have your heating and cooling in your basement.
Out in the west, it is very common (until recently) to have the AC and heater or swamp cooler on the roof. It is also not only common, but CODE to have the roofer lift the legs of the units and put the shingles under them and then put some tar around the legs. This is the normal and legal practice!
To the OP: Is a 50 percent deposit even legal in your state? Where I live a contractor can't take more than 10 percent for a deposit. Was he even a licensed contractor?
Second, did it pass city inspection? He did pull a permit, right? Don't pay anything until the inspection and ask the inspector about the cooler. You definitely got a bad job, it's just a matter of if it was not done to code and he will have to fix it.
Whatever happens, given the obvious lack of attention to detail by this guy, I would get a reputable roofer to come out and do an inspection to see if he thinks there is anything that is going to cause big problems. This shouldn't cost more than 100 bucks and is well worth it after dealing with bozos like you did (I had a similar situation and had to do the same thing).