Hi Michael, it sounds like your on top of the problem thanks for sharing you issue, we have an 06 Thunder and this model has a very nice fill about 1.25" in size that allows us to fill from the top of the tank this was a great improvement. We also have the auto fill but the rig is the same as yours in this respected it would take hours to fill if empty.
I know a lot of Beavers had added a modified fill port. You might want to take a photo and post it!!