To confirm what the other guys are saying here, on a relatively mild 347 build up (400 crank HP), MM&FF tested unequal shorties, equal-length shorties and long tubes (all 1 5/8ths primaries) and long tubes with 1 3/4 primaries with dyno runs on the same engine. All 4 sets made within 3 or 4 HP and torque of each other at peak. However, the 1 5/8" long tubes were MUCH stronger at low rpm - at 3000 they were making almost 40 lb-ft more (the 1 5/8). Unfortunately the goobers running the test seemed to miss that "minor" difference, and didn't run the test at any lower rpms.
The bottom line is that it's really a case by case. Primary size, collector size, collector type/configuration and length can really have an impact on a higher output motor. Most folks find out what works best by experimenting. I suppose some of your custom cam designers might have the ability to model some of those details to try and help you predict what's gonna work best.
In general - long tubes are gonna be your best bet regardless. On milder motors, even if the peak isn't much improved, the bottom should be. And as power levels increase, they'll show more benefit. Wish there was room on mine...