Let me see if I understand you correctly.
You removed the Raymarine FF to install a Furuno FF. The Ray was originally wired to a fuse panel or bus bar. Upon initial installation of the Furuno, you connected the original power wires from the Ray to the Furuno (assuming you cut and spliced the wires or something to that effect).
You later rerouted the Furuno to draw power directly from the battery.
My first guess is that in the rewiring process you either knocked a wire(s) running to the guages in question loose. Probably a ground wire on the negative bus/fuse panel or actually at the battery. Being that every boat is wired differently, it's a tough call. Get in there and start tracing wires.
Try reconnecting the trim pump and see if your gauges work then. Maybe they are somehow combined on the same circuit??
With all that in mind, I'd have to (as well as most others on the board) recommend against wiring the FF directly to the battery. Hook it up to a fuse panel and trash the inline fuse. That's a much more reliable method. Man, if Thom were still around, he would have a heart attack!
Good luck and let us know what you come up with.
You may also look into istalling a
Navman fuel flow meter on your rig. I put one on mine and have found I never look at the fuel guage any more. The Navman is deadly accurate and makes the analog fuel gauge worthless (well, it fills the 2 1/8" hole in my dash nicely

)
Brian
http://userpages.umbc.edu/~bmille4/sirreel/index.html