Steve, the canopy glass vs clouds is a known issue with FS9 models in FSX, nothing afaik can fix that. About the fuel inbalance, please check the [fuel] section in your Aircraft.cfg:
[fuel]
//Longitudinal (feet), Lateral (feet), Vertical (feet), Usable(gallons), Unusable (gallons)
;1807 gall intern + 2x 370 + 1x 600 ext
fuel_type = 2
number_of_tank_selectors = 1
electric_pump = 1
Center1 = -6.0, 0.0, 0.5, 1163, 22
LeftMain = -8.5, -6.0, -4.2, 322, 7
LeftAux = -8.0,-11.3, -6.3, 372, 2 ;ext wing ext tank 370 gall
RightMain= -8.5, 6.0, -4.2, 322, 7
RightAux = -8.0, 11.3, -6.3, 372, 2 ;ext wing ext tank 370 gall
External1 = -10.0, 0.0, -6.5, 602, 2 ;ext belly tank 600 gall
fuel_dump_rate = 0.009 ;MOD Percent of max quantity per second
As you can see, the wing droptanks are LeftAux & RightAux, make sure the underlined offsets are as above. External1 is the big belly tank. PM me if this does not fix the problem.
cheers, Henk.