"But can the Breaker for the FP controler be in the Switchgear with all the other loads??"
I have seen FP feeders in existing gear, as it was allowed some time back (I have been told). The feeder conductors are supposed to be physically barriered from the other conductors within the gear. There are three older whse bldgs in my Twp. that the insurance company is requiring that the FP wiring be brought up to current codes. They were given 120 days to comply, or be dropped for insurance.
"Can the cable from the Switch gear be in Cable tray with all the Normal power feeds???(2 hr required fire rateing))"
Without cracking the book open, I'll vote no; Are you saying that it now has a 2 hr rating?
"To make this Correct Where should this Normal feeder (on back up Generator be picked up??"
My first choice would be to connect on the secondary buss of the xfr, before any OCP, and treat the conductors & raceway as a FP 'service' into the controller/transfer switch.
At the begining of your post you said the FP is dual prime mover, diesel and elec, correct? Am I reading that right? As there are two prime movers for the FP, why the BU genset?
Let's see what other opinions are made.