The cab needs to be on at initial set up though to be sure you are clearing the firewall and all. And while the motor is setting there in the mock up stages you need to check for radiator clearance too, the Ford V8 is long and can be an issue with the radiator so don't take anything for granted.
Honestly, the motor being exactly in the middle has little to do with vibrations or anything else like that for that matter. There are many cars over the years from the factory that the motor wasn't in the center, look at a front wheel drive car, it's sitting sideways! The big block 67-69 Camaro motor is off to one side about an inch! The vibration would come from something out of balance, like the flywheel, clutch or driveshaft would be my first places to check, and the most common to be out. The flywheel and clutch assy are sometimes "clocked" together so you need to reinstall them as marked.
If you are measuring side to side at the crank in the front and transmission tail shaft in the rear to "control points" (points that are exactly the same side to side) on the frame you are good to go. Making it "somewhat" even is what we are talking about here. If the whole motor is off to one side a little it isn't a big deal.
Having the proper pinion angle to promote the U joints bearings to spin properly is next thing to think about. But with the motor about where the old one was this should fall into play. If it is level and the tail shaft on the trans is about the same height all should be good.