Could be fuel supply, or fuel mixture.
Would be worth checking the condition of the plugs as that can give clues towards mixture issues. Too rich and you'll get carbon deposits which can lead to tracking over, reducing or removing the spark. Too lean and the burn temperature will increase which can cause electrode erosion or insulator cracking/failure if it exceeds the operating temperature range of the plug. There are lots of reference charts on t'internet, e.g. http://www.aa1car.com/library/reading_spark_plugs.jpg
Also worth checking the air intake system, making sure any joints are sound etc. as that can adversely affect the mixture.
On the fuel side (again not familiar with the Bonneville) if you can visually inspect the filter to make sure it's not fouled, that's a good place to start. An overheating fuel pump is fairly rare, but modern designs tend to use the fuel to provide cooling to the pump so a fouled filter will mean a greater amount of absorbed power is required to pump the fuel which equates to more heat to dissipate.
Hope this helps
