Our Latest Saga

Our latest saga is bigger and more expensive than we ever anticipated! 
When we bought this house we knew that the water heater was 13 years old.  So, we got a quote from the same plumber that did our irrigation system.  We wanted it replaced before it burst and potentially destroyed all the drywall I just spent 3 weekends putting up in the basement for my workshop.
Since the plumber was going to be doing the water heater, we figured it would be convenient and cheaper to have him run a gas line (yes he has a gas license) for the stove.  Since we heat the house with natural gas we wanted to upgrade our old almond electrical stove to a new gas stove that we purchased at 30 % off from Lowes. The stove is original to the house (1993) so the new gas one would save us monthly on our electric bill. 
And since I am anal retentive and forward thinking, he also noticed that the furnace was drawing air from the basement instead of from the outside.  Not a problem when your basement is unfinished, but since spray foamed the workshop side, we eventually would spray foam the entire basement and build a couple of rooms down there (TV Room, Craft Room, etc...).  Again, killing 2(or 3) birds with one stone (plumber) seemed to be convenient. 
Pretty simple and straight forward?  Run gas line to new stove and install new water heater; quote $2300.  I don't mess with gas, plus NH requires a gas license and inspection and permits, we wanted it done by a licensed plumber.  Check, check, check.
This was last week. Water heater is installed and running great.
In the process of doing the intake on the furnace, they notice that the combustion pressure switch was bypassed!  They replace the switch and still the furnace will not fire.  Looking at the manual, the exhaust requires a 3" PVC pipe, but the original installers only used a 2" pipe.  Not a big deal.  During their 2 days of troubleshooting and taking tons of measurements and checking out the system, they find that the furnace is hitting the high limit and setting off that high limit switch.  This means that the temperature is going too high for the heating element and shutting off the element as a safety.  The blower continues running, but then only circulates cool air.  This will not work when the temperature outside is 0 degrees.
The plumber said the furnace is too large for the duct work or the duct work is too small for the furnace (however you want to slice).  Oh and the A Coil (Air Conditioner coil) is too small for the furnace as well.  No matter how you slice it all of these problems equals $$$$$$$$$$$$$$$$$$$$$$$$$$ that we weren't intending on spending!! 
The manual states that the supply duct work needs to be 390 sq in and the return needs to be 440 sq in.  Our supply is 231 sq in and our return is 264 sq in.  Only about 33% smaller than it needs to be :(
The plumber is looking into the least expensive option.  But may require a new furnace, a new A Coil, more duct work (with drywall work upstairs) or any combination of these things!!!
So, the original contractors mess up and now it is our problem!