Bummer it didn't work out this trip. After looking at your trip thread and seeing all the homes on stilts and knowing the fuel tanks are underground I can see potential fuel problems as well.
Sometimes simple is better but unfortunately bikes seem to be getting more complicated. Maybe a KLR is in your future again but I for one could not go back.
In all other areas that 990 is a great bike, have you thought about a work around so that the filters are modified in a way to make them more accessible and using a filtering funnel like this one?