Fuel Tank Problems

I have a 1989 Wellcraft v20 CC Fisherman . My problem is that I can not get fuel from the tank to the 200 hp Yamaha OB. I replaced the fuel line 2 years ago and installed a water seperator . Last year each time we went out the fuel ball would flatten and the engine would stop . To correct it we would reverse the ball and blow air through the line to the tank. This would allow us to run for another 15 minutes. I think I have to drain the fuel tank and remove the pick up tube from the tank to find out what is causing the blockage . Has anyone done this before as getting to the pick up without removing the floor pannel looks very difficult Advice would be welcome .