So I got into the lower tank and it is pretty much the same as the top one. I ordered a MR FUNNEL which is the same as the baja
funnel etc and I took about 7 litters off the bottom of the top tank and ran it through the funnel. I would say I probably got about 5mils of water out of that so not a huge amount but some none the less. So the next step will be to do as suggested and setup a polishing system running the fuel through the funnel and the normal filters also. The up side however is that the inch pipe that I took the fuel out of from the bottom of the top tank had zero sludge in it so I am hopeful that there is no bacteria growing in there yet. The fuel smelt a lot better after being run through the funnel but still had a yellow look to it. Hopefully its not as bad as I think as the motor
was still running fine.
Will let you know how it went after the polishing for those that are interested. Thanks again for every bodies suggestions and help.