I hope the 90K is the output or it's truly undersized! Even so, it's quite common to oversize furnaces beyond the calculated heat loss by 20-30%. It's also possible the heat loss calculation is low, it's really just an estimate, and part of why the furnaces are oversized. Even if it is undersized, it would not significantly alter your energy costs. Costs are dependent mainly on the home's overall insulation and the furnace efficiency, the capacity and running time is not a big factor.
Changing ductwork will better distribute the heat, but if more heat is leaking out than the furnace can generate, it will not help. While a larger furnace will better heat your home, it will not help your energy costs. If your costs are out of line for your type and size of house in your area, then more heat is being lost than is typical. In the long run, you are better off preventing heat loss than generating more heat.
There are energy consultants in most areas that have the proper tools and equipment to advise you where most of the heat is being lost and what could be done to most effectively reduce heat loss.
It sounds like you have an ECM "constant flow" blower that ramps up output as high as necessary to maintain the set airflow (aka an ECM constant torque motor). A MERV 11 filter is too restrictive for most residential systems. In this case, the motor would compensate for the restrictive filter by running harder and hotter to maintain the airflow. Switch to a MERV 8 filter (it's still a pretty good filter). If your system delivers more airflow than you need, then also set the airflow selector switches in the furnace to a lower setting. Obviously the air filter should also be changed regularly before it becomes plugged or the blower will again ramp up to a very high level to compensate.
EDIT; Specifics related to OP's situation:
It turns out OP has a very high performance MERV 11 filter which if correctly matched to the system might be OK. The stamp on the side of the filter states "Airflow Capacity up to 1400 CFM." In reality I would expect this to mean this filter might be successfully employed on a system with a 3 ton cooling capacity (3 tons / 1200 cfm). It would not work for a larger system.
I found more detailed information on an air cleaner that uses OP's media here:
http://www.cleancomfort.com/assets/Brochures_SpecSheets/Filtration/SS-AM11-3225.pdf
The referenced unit above uses two (2) AMP-M1-1056 filters and therefore handles twice the airflow of OP's setup. In my experience a pleated filter is near its end of life when the static pressure drop reaches about 0.2" WC. Looking at the "AM11-3225-5 Pressure Drop vs. Air Flow Rate" chart on page 2, one sees 0.2" static pressure loss corresponds to 2600 CFM for two filter cartridges when new. So according to this chart, 1300 CFM would be the max airflow through OP's one cartridge when new and if one were to run the filter at that high a flow it would need to be changed very frequently (at least monthly?) because it would become more restrictive as it filled with particles.
My conclusion: If OP's system does not exceed 3 tons / 1200 CFM and OP changes the filters monthly (normal intervals of 3-6 months are plausible if the system is 2 tons / 800 CFM or smaller) then the existing setup is probably OK. Otherwise switch to something less restrictive.
Best Answer
If by airflow you mean the flow of heated air through your home, then I would say yes: a furnace needs to be sized based on how much heated air can be pumped through your home. If your furnace is enormous, and your ducts are small enough that the total air flow is too low, then the furnace won't be able to transfer enough heat to the home air, producing too-hot output air while reducing the furnace's efficiency.
However, this does NOT mean that no high-efficiency furnace will work with an older home with few/narrow heating ducts. You just have to find one that's appropriately sized.
A side note: furnace installers have a tendency to over-size furnaces and boilers, on the theory that too big is better than too small. The truth is that many (most?) furnaces and boilers are larger than they need to be. So, get a heat loss calculation done for your home and then proceed from there.