I would say that pretty much the later head will outflow the older one. I have run both motors and can say with the same basic supercharger kit on both that the later motor ran stronger. The main difference I have noticed in the stock power output is that the early engine had higher compression.
The easiest thing to do though is go have both of them flow tested on a bench.
I also was comparing the c36 head the other day to standard 3.2l head and the only noticeable difference in that head was the exhaust was ported out to gasket match. The bowls on both the intake and exhaust were cleaned up but that was it and the head flows significantly better than the 3.2l.
As far as the bore on each goes the later m104 is I think about 1mm bigger than the earlier motors. The stroke is the same. In fact I have stroked a 2.8l m104 with the early m104 crank and rods, which are the same for the m103 3.0l also.