Eddy-
Think of it like this: you're not going to jet the individual cylinders differently, so taking reading after the collector is really the best you are going to do, as it pertains to jetting.
However, that doesn't mean everything is magically the same in all four corners of the engine. Some minor devation is normal, but if you are rich in one bank and burning cleanly in the other (with the same jets), I'd say you probably have a vacuum leak, a linkage problem, or something else going on in one side of the engine or the other. I'd sure dig deeper-- but I wouldn't ever jet an individual bore differently than the others.
Jetting is the last thing I do when I'm tuning the car: after I make sure the valves are adjusted, the timing is set, and the ignition is advancing properly. Paying really, really close attention to the linkage from idle to wide open throttle is equally important-- I've yet to see a hex-bar set-up that is perfect out of the box. Generally, if they are synced at idle, one carb or another leads pretty significantly to WOT. You can straighten this out by re-drilling the holes in the arms of the linkage.
I'm no ace. I've chased a jetting problem for weeks that turned out to be a problem with the CDI box, a bad distributor cap, timing scatter, or some other problem. Somebody a lot smarter than me once said that 95% of all jetting problems are ignition, and I've found it to be true.
one thing that makes me look a lot smarter than I really am is that I monitor all four cylinder head temps. I've found ignition, mechanical, and fuel problems in an individual cylinder long before I would have otherwise with the gauges (when the temp in one cylinder drops off-- there's a problem). If I'm plugging an idle jet or a plug wire has come loose, I know which one it is before I even get out of the car. That alone makes what I'm doing worth it.