Anyone see any problems with how I want to install my air/water exchanger

The best way would be to have a sheetmetal shop fabricated smooth, tapered transition fitting. Your furnace is moving air thru a 493 sq inch duct, you will be reducing to 440 square if you block off the overlap. Not ideal for airflow and it may cause noise issues and over-heating when it runs on the burner, due to restricted airflow.

Was the heat exchanger sized to the load and required CFM required?

Wouldn't that reduce the heat exchanger's efficiency?

From what I understand, correct me if I am wrong, the heat exchanger will transfer the heat from the water, into the metal, which heats the air.
If you put it right on top of the furnace (I'm assuming the furnace's heat exchanger), it now becomes a larger area that will be heated and likely
will turn out to be more of a cooling effect.

I may be wrong.

You are not going to get the most out of the HE no matter what you do...you are losing 5" of surface area.....You will probably be ok as long as you have something nice fabricated that will mate the HE in place and seal off the connection well...

I contacted a HX supplier recommended by the folks here. I told the supplier the duct work dimensions, fan CFM, desired temp drop of the water at a nominal input water temp, and I think the gpm. This basically tells the HX expert how much energy you want to dump into your existing duct given the CFM of your blower. I wanted a 30 degF water temp drop with 180F water in with the fan on. The HX supplier then computed the required HX thickness to achieve all these goals with my existing fan/duct. This was a 10-15 phone call to the HX supplier. It showed up in a few days and matched my duct perfectly. This is what Bob was implying. Maybe the thickness and area of your HX is designed for your boiler output and fan CFM. If your boiler/HX supplier didn't ask any questions about your fan or duct.... I'd be worried. This is a huge deal. Like putting undersized tires on a dragster. You want to get all that capacity out of that boiler. Cheers from a '72 PSU grad.

Boy, been a long time. I don't have my supplier list here, but I think Northland. Google water to air heat exchanges. Maybe one of the pros will chime in. See what you find using the Hearth search.

Let me make sure I understand... You picked a boiler with an energy capacity to meet your home's needs, but you have no idea if the device that transfers the boiler's energy and puts it your home is matched to the boiler, pump, and fan.