Hi Dave, Welcome to BOBII and the BOBII forum and community. Thanks for the kind words about BOBII. Here is a link about the BOBII developers:viewtopic.php?f=48&t=9483
Is the BOBII picking up and licting all your CH controllers (stck,pedals, and throttle) under Options->Controls , Input Dive pull down list? It will need to list all your input devices so you can select them and assign them.
I have the CH Combat stick and CH Pro Pedals (I do not have the throttle but many other players have it set up so it is not a problem you just assign your CHThrottle to the correct axis).
Here is a pic of my set up you can use to set up your controllers (I hope). The User manual shold also provide you information under the controller chapter: