Hi Veek,
We've run the bigger Ford alternator, in the interest of providing more voltage at low RPM. So it can be done, although you should check your pulley diameters too. Make sure the alternator pulley is as small as possible.
I think most guys are running March pulley sets as they are top quality and come with easy to adjust brackets, my concern is the crank pulley diameter as it's quite a bit smaller than the stock Ford. While intended to save horsepower by reducing the speed of the water pump, alternator, air pump, A/C pump, power steering pump in the case of CAV GTs the current demand at idle, with the A/C, headlights, cooling fans, interior fans, high pressure fuel pumps, ignition box etc. is more than an underdriven alternator can provide.
So your counting on the battery to carry the load while idling, that's tough too because once your voltage drops below 10.5 volts the gauges start acting up, ignition boxes can get misfire. We're probably asking for 60 amps at idle with all loads on, no alternator can provide that below a minimum RPM, hence my concern about pulley diameters.
Try bumping up the idle at full electrical load and watch the volt gauge, you'll probably see 12v by 1000rpm and all the gremlins will disappear too. Here's a pic of our big alternator install. Hope this helps.
Cheers