BTW, I'm not bragging, I just wanted you to know that things will get better, and you will have something to write up at the end! :)

I was in exactly the same situation last year. I had been doing PCR on the same 5kb of DNA for months and got one fraction out of the five I wanted.
So I sat down with my supervisor and told him that I really didn't want to do this anymore! And he agreed - there are far better uses of my time. So I think you should do this. Ask your supervisor if there's any other experiments you can do to show the same thing or if you can go in a slightly different direction.
I felt totally depressed about my project this time last year (I'm in the middle of my 2nd yr now) - I had no results and no explaination as to why. But over the last couple of months everything has started to go right for me - I've so many reproducible results now I can barely keep up!

Firstly, congrats on getting your paper done :)
I reckon that if you don't want your secondary supervisors name on the paper, then don't put it on!! Talk to your primary and tell him you agree; you feel that your secondary hasn't made enough of a ccontribution to be an author. Maybe mention your secondary in an acknowledgement? I agree with shani - let your supervisors slug it out! :)

I'm funded by the BBSRC and (so far!) haven't had any problems. I'm paid quarterly, and my money was there when I started at the beginning of October. I was impressed as I always had problems with my student loan going into the same bank account but the BBSRC are managing without a problem!