The answer to the first question is all 348s had small port heads & intakes and all 409s had large port heads & intakes (except 1961 409s which used heads with part number ending in 586 which are small port heads). Large port heads have part numbers ending in 690 or 583 (except Z11 heads). There is a listing of 348 and 409 head part numbers and discription on this site: From the Site Menu go to 348 & 409 Engines > Casting Codes > 348/409 Cylinder Head Casting Numbers. Intake manifolde are listed also.
The answer to the second question is it is possible to use large port intake on small port heads but not the other way around. The large port intake manifold needs to be modified by removing the four sets of "ears" by the bolts between the adjacent intake ports. Some say the the large port intake with small port heads has a port mismatch that hurts performance and that's probably true but I ran a truck 409 with small port heads and a large port 2 x 4 intake for three years and was satisfied with the way the engine ran.
348 heads were small and smaller. 58-mid 60 were all small. In mid 60, the 1147 head came out with larger runners and ports. These same size ports and runners carried over to the 586 heads for 61, 333 truck heads for both 348 and 409 through 65, and the 817 heads used on the 63-65 340 hp 409 with hydraulic lifters.
The first real large port heads were the 690's in late 61 followed by the 583's in 63, and I won't even go into the Z-11 heads.
Keep in mind that there were many different casting numbers of 348 heads that keep turning up through 61, but the ports and runners were still considered small compared to the 690 and 583 heads. So far, I haven't been able to determine what the differences in all those 348 heads were, but it may have mostly been changes in metallurgy, since the design didn't seem to change.
Yeah, those 817 castings from the 1963-1964 era were "small port 409 heads" and were matched with (I think I am correct here) cast iron intakes that delivered 340 horses. A sort of detuned 409 for those who just wanted a boat load of torque. Clyde is right in that the 690 and the 583 heads ushered in the "high port era" from late 1961 until mid 1965. Pretty sure all those intakes, whether single four barrel or dual fours, were all Winter cast aluminum intakes with larger ports.