The part numbers from the TM are the manufacturer part numbers, with slight differences. But for all intents and purposes are what you want.
The part numbers you want for your project are as follows...
97-3106a32-7s This is the larger connector that will screw into the back of the control box.
97-3101a32-7p This is the larger connector that will screw into the wiring harness left on the generator after you relocate the control box.
ms3106a20-22s This is the smaller connector that will screw into the back of the control box.
ms3101a20-22p This is the smaller connector that will screw into the wiring harness left on the generator after you relocate the control box
The parts that start with 97 are the civilian version of the connector. The ones starting with ms are the "Military Standard" connectors because that particular pin/contact configuration in only available in the military product line.
On all of those part numbers you will need to call Newark and get quotes on prices for them. They are not listed currently in their catalog but they will be able to get them for you. When they get the price quotes from Amphenol, they should assign their own catalog numbers to them. Once this is done, please post up the Newark catalog numbers, corresponding Amphenol part number and quoted cost for each part. That way we will have the information for future reference, in case someone else wants to do this same kind of project.