I have been quoted $4200 for duct work. Is this average? Seems high to me. My home is ~2100-2200 sq ft. 1 story except for a bonus room over the garage which they DO NOT plan on touching the duct work for since in the future I'll do a mini split anyway.

The contractor will:

Raise up the system in the attic
Redo the phelnum, main trunk lines
Install return, none exist today
Install dampers in the supply lines
Replace SOME of the supply lines if not sized right
Add sometype of electric shut off to the system
Fix the 2 zones on the system.

Is this a decent price?

lets talk about what you have
supply plenum (tall metal plenum with flex or hard pipe ducts)or trunk line with ducts?

return air..you have to have some type of return for the existing unit to have worked. maybe not a return plenum but at minimum a return duct.

part of the cost may be to installzone & zone dampers?
but it wouldn't make sense to have zone dampers
& manual dampers.cost to hvac company would be 1K at minimun for zone board & dampers. if true zoned system then you would have one tstat per zone.

and this:
Replace SOME of the supply lines if not sized right.
so are the runs sized right or not?
can they not determine this prior to bid?
with flex you could roughly figure $200 per supply duct.
this doesn't include new supply box if duct is upsized.
and if you upsize duct & not supply box and grill you have not accomplished much.

can you take some pictures & let us take a look?
flex duct..silver, black or gray?
do you have trunk lines made of metal or ductboard?
how many supplies do you currently have?
where do you change your filter? at ceiling?
(this is your return air) it may not have a plenum
but at leas it will have a flex duct back to the unit.
what is your location?

I'd get more info before spending this amount
on a sketchy description of what is to be done.

its not just adding ducts..you have to determine what cfm
(cubic feet per minute) your unit supplies.
@ 400 cfm per ton a 3 ton unit would have 1200 cfm
to divide among the rooms. duct size is determined by
size of room, amount & type of windows shading etc.
there is a method for this.

static pressure, duct leakage, return leakage all factor in.

I know I ask a lot of questions..and think..its not
even my money being spent!
I'd require more info.
give us more details & maybe we can help.

best of luck