Steve

You have CAN on the storm, right? I would suggest you find a controller with CAN output and use that instead of a 0-5v signal. Can is not affected by "ground offset". But yeah, age might be a factor also.
There are several vendors offering these.. AEM, Motec, KMS, Emtron, Ecotrons to name a few

You can run any sensor you like as long as data for that sensor can be found. If it isn't listed in the dropdown menu then you need the correct data for your particular sensor. Google will probably be your best friend in that regard. Or testing...

You dont need to do anything to the cam sensor other than check that the cam synk signal and one of the crank theeth DONT pass the sensors at the same time. Preferably you should set the cam sensor so that it triggers halfway between two crank theeth.
To get timinglight and crank marks to line up you just adjust timing offset in the software.

You are right. You can do it like i did then. Use a GP output  with the conditions of your choise. Pictured is how MY second pump is switched on