Since I have some experience with Naval/home boilers, and radiators, I'll toss in a couple cents. Joe, I don't have experience with wood burners, but I expect you know from the ash if it's burning right. No different than looking at coal clinkers I guess. So I'm assuming the wood is burning fine. If you're using more wood there's only 3 possibilities. Your new boiler either has poorer heat transfer than your old one, or the pump isn't pushing enough water, or you're losing too much heat up the stack, In any case, too many BTU's up the chimney. With a bigger firebox you might be loading too much wood in the there.
After I bought a house with a gas boiler I didn't like how much heat was going up the chimney. I throttled the gas supply to about half of what it was, and it reduced my gas usage quite a bit. Longer "on" cycles, but worth it. The pump doesn't use much juice.
If your new pump has lower capacity than the old one, and is out of spec for the system you won't get as much heat transfer at the water jacket or tubes. I don't know how they spec that for home boilers, but it's a factor, especially with your long piping runs. Restrictions - you mentioned a maybe backwards zone valve I think - will have an effect on heat transfer too. And check that your damper is operating properly. Anyway, the guys who installed your boiler should have some answers. Maybe. Some installers only know installation.
Harry, you got all the convection thermodynamics right. Every cast iron hot water radiator I've seen it probably doesn't matter enough to have the water inlet on top to justify the cosmetics of the long pipe. No doubt you get an edge though.
If you see one hanging on a wall with a top feed it's probably only because the piping runs made that the sensible way to do it. Not that I'm a "radiator engineer" but I've had some apart.and put them together.
Each section has the same size passage on top and bottom. The end sections have legs, and threads cut in the holes on one side to take a plug and nipple. And a vent hole tapped. All the inner sections are identical, and all sections are connected by push nipples. I think the plumbers put them together on site. One I replaced took 3 big guys to move it out of the house. I've only seen inlet/outlet on the bottom in homes, including mine. They always heat from bottom up, due to natural convection in the sections. Pretty obvious you're not circulating the coolest water back to the boiler. It would be interesting to measure the flow and convection for both top and bottom inlet, It would be more energy efficient if they were designed to pass all the water through from inlet to outlet. IOW, enter at one end of a section, exit only at the other end of the section. Then you'd be getting cooler water at the boiler and better heat transfer. But you'd always need an even number of sections to have in/out on the bottom, You'd have to have more castings. That's not how they did it. Hey, coal was cheap, so why bother. They work pretty good. I always liked hot water heat, but now that I've adjusted to forced air, I don't want to go back.
--Vic