I should have added that the recommended systems were Lennox XP17-036 (17 SEER that comes down to 15.8 SEER for reasons that I forgot), and XP14-036 for 15 SEER, both with 10kw heat strip. The XP17 also comes with an air cleaner and a fancy iComfort thermostat (that I don't truly need).

You have a two HVAC systems for your two story house which is relatively young. You should not be experiencing rooms which are too hot or too cold. I suspect you have significant duct supply problems. The supplies in the attic likely should be done with a combination of a hard main supply and R8 flexible ducts. The downstairs ducts should be sealed wherever it is practical.

You should make adding more insulation to your attic the first order of business. If you are handy you can do this yourself. You want an minimum of R30. More is better. You also should seal the attic hatch. You can buy a cover or make one yourself. It is not hard.

I am a little suspect of the Manual J calculation. A 3300 sq. foot house built in 1994 should not require 6 tons of cooling. Do you have a copy of the calculation report? Did the contractor explain it to you?

I would not replace the gas furnace with a heat pump. What are your gas and electric rates? Is the garage heated? If it is, my vote would be to install a 95%+ efficiency furnace when you are ready for replacement.

I'd invest in the duct sealing (including returns) of both systems. see what that does as for comfort &
air flow. this is one investment that quickly
pays for itself. paint on mastics or true mastic tapes
are the only sealants I'd allow.

there is nothing wrong with ductboard & it is not
an inferior product. a well installed, correctly
designed & sized duct board plenum will
perform just as well as a sheet metal plenum.
I have to admit...statements like 'inferior product'
send up a red flag for me.
IMO it is a short way to say.."I'll charge/make
more to tear it out & replace it"
that he wants to increase size of the upstairs
system is the second red flag.
bigger isn't better.

take a look at it yourself. is the ductboard plenum
larger in size at the equipment & reduced down
towards the end of the plenum? is it in good shape?
are the flex runs straight? are the ducts well sealed
at the plenum? take a couple of pics & post.
we can't see as well as you can...but we will look.

now if there are comfort issues & obvious problems
with the supply plenum & ducts...then you'd have reason
to think about re-design. but often comfort issues
are solved by installing manual dampers so that you
can adjust air flow and by increasing size of a duct
or two. crimped or compressed ducts reduce air flow..
but are usually easily fixed or replaced.

30% duct leakage isn't uncommon at all. it is more
the norm than the exception.

so if you invest 2K in duct sealing & then still feel
the need to replace equipment..
but I'd like to see pics before going further.

before adding insulation, complete all work in attic
including duct change outs. sealing or modifications.
any equipement change outs should be completed.
then..and only then..does insulation install need to
be consitered.
adding insulation prior to any work will make it
more difficult to work, insulation will be compressed
as work is done, and any insulation moved to access
work may not be properly replaced.

before insulation though...air seal. supply grills inside
the house and bath vent fans cover oversized cuts
in ceilings. recessed lights that aren't air tight allow
leakage from attic into house.
accesses into attic will also leak, and should be
built up around access to hold insulation in place
as access is opened.

blower door test should have provided list of
areas of infiltration. what were the blower door
numbers (example 5000 cfm @ 50 pa)??
was duct leakage test done at same time?
what plan of action/information/advice did auditor
give you @ time of audit?

I'd suspect that load calc wasn't done and equipment
is oversized.

in my area we ususally put gas heat on first floor
and heat pump on second floor. heat will rise
in winter to suppliment heat pump heat on second
floor.

do you have a prefrence as to gas or heat pump?
is one cheaper/higher than the other to make
choice for you?

I'm glad to see that you are willing to invest some
time in determining what is best for your house.
rather than just throwing $$ at newer bigger
equipment it makes sense to evaluate what you
have. take time to make decisions that will
provide comfort and savings.

best of luck.

My mistake...the hvac company did the blower door test...
this company is the one who said ductboard was inferior,
wants to upsize second floor unit...and tested ducts.

since you are needing advice on what investments
to incorperate in your home...what about an
independent doing the testing, making
recommendations & verifying everyone's work?

the best gain for you is someone not selling you
products, that installs are verified & tested,
and that he/she can offer unbiased information,
that is specific to you & your house.

energy raters test both house for leakage,
blower door test and ducts for leakage with
a duct blaster.
most can pinpoint leaks of both house & ducts.
you get recommendations of how to seal &
verify that work has been done correctly with
final inspection & testing.

resnet.us is the main source for energy raters.
duct testing is part of each rating.
this will let you know where you are now..give
you recommendations & paybacks of upgrades &
verify on end of job.

bpi has energy auditors, not sure if they
do duct testing as part of audit, or if they
re-test to verify what was actually achieved.

just something to think about.
advice on a local level from someone with no
dog in the fight. an independent unbiased third
party hired by you.
you are getting ready to spend a good amount
of cash...do so wisely.

best of luck.