Only the right builder can alleviate the 'infamous' 347 problem. Not all 347 combinations are corrected. The use of proper tolerances, oil support ring orientation, skirt design, all become something that needs to addressed. To tell someone it is a wives tale, is a bit misleading. Then again, telling someone that 347's are junk, is along the same lines
Frosty GT - Read the link in my signature for some information on the differences. It may help your choice. Either way, you have a mustang and your wanting to pick a nice combination of parts

Seems like you are on your way
Now, the 347 does have a slightly worse rod/stroke ratio, but it is extremely small. Back in the day, with the 3.4" stroke (347), rotating assembly manufacturer's only made a short piston (1.090") that had the wrist pin interesecting into the oil ring land. This causes some unneccessary blow-by at the time. Now, companies like CHP (Probe products), DSS, have created a shorter rod, 5.315" instead of the old 5.4", which in turn let's one use a taller piston, a 1.175". By doing this, they kept the same 3.4" stroke and with the taller compression height piston (1.175"), it kept the wrist pin and the oil ring land from intersecting. Therefore, it is designed like the 331 or 302
I would go with a 331 if you want to be different, which is totally cool! Or if you want to go with high boost or nitrous use later...
Either way, you pay for it, and you get what you want. Whatever makes you feel at ease.