Bill,
The heads and intake must be matched. All 348s, '61 409s and '63-65 409-340hp used a smaller intake port design, therefore the intakes had to be configured to match the heads. Although the '61 '09 had a hi-rise aluminum intake, it still had the small port design. When '62 came along (not counting the service parts released around July '61) the heads were different castings with taller (bigger) ports. The only intakes that will bolt up to those also have to have the taller ports. Visually, it's easy to see the difference; the upper bolt hole between the ports is nested between the ports (small port) and the casting goes around the hole. On the large port heads (690s and 583s) the ports are square on top and the bolt is above the pair of ports.
The exhaust side is essentially the same and ANY 348-409 exhaust manifolds will interchange. And both 348 or 409 heads will bolt to any "W" block. Except for the early '58s (which had no provision for plug cooling holes) all the water passages and bolt holes are in the same place.
So, the simple answer is any "W" head can be put on any "W" block, as long as the intake matches the head.
Sorry, I get carried away....
Verne