I'd suggest before you go tearing anything apart, know the static pressure and CFM's the system is producing, and verify the system is doing what it's supposed to be doing and not make an assumption it's air turbulence (yes, easy assumption to make, but it could potentially save another headache). I could be wrong, but I don't think the OP has given that information.
As a precursor to answering this question,,
a) I have talked to over 6 local HVAC companies.
b) I have personally talked to over 20 HVAC technicians.
My conclusion is that the local HVAC companies can
A) do some tin knocking,
B) physically place new components.
C) silver solder copper lines.
D) get operating pressure of the HVAC gas in the system close enough.
I also feel that the local HVAC companies,
E) have almost zero understanding of the NEC (national electrical code)
F) have ZERO intention of reading the installation manual
G) have enough knowledge to do a basic thermostat install,
BUT, have almost zero capability to customize thermostat settings for an individual install.
True, I have not given the CFM's and static pressure.
If I use the previous system as a baseline, (it worked perfectly from 1977 to 2020)
1) the CFM air flow of the new system appears to be identical to the old system, or very close.
2) the tonnage rating of the two systems are identical.
3) the comfort level of the new system is adequate, not perfect, but, the old one was not perfect either.
4) in about 1.5 years of operation, no occurrences such as unit freeze-up has occurred.
So, based on my satisfaction with the new system, my only major drawback is the noise.
I am sure I could get the CFM readings of the system, with a little YouTube help, and buy some equipment.
I could build an adequate manometer, and get the pressure.
Since the big issue that I see is the noise, and my hand (felt vibration) has isolated the noise to the plenum,,
I feel that the easy fix is a suitable block-off transition in the plenum.
The only reason I have not started tearing out the plenum is that I have one stumbling block that should be resolved within a week.
So, I started this thread to help me get my ducks (NOT DUCTS!! LOL!) in a row,
for hopefully finding the easiest way to install the transition.
If the air handler were located directly under the "T" fitting that is part of the original ductwork, I would get the plenum remade.
The MAJOR problem is that the plenum also has a 3.5" sideways offset.
The air handler can not be easily moved, that plenum would be almost impossible to rebuild from simply giving a guy dimensions.
Therefore, hopefully, I will be able to install a block-off plate.
If I install the block-off, and the noise is resolved, I would happily pay a duct company to come out and make a new plenum correctly.
The problem is ,, I am POSITIVE that a local company will end up charging north of $500 to make that new plenum.
That $500 price is based on the new price of labor, transportation times, figuring in at least 3 visits to get it right.
If I do not tell them EXACTLY what to do,, I will end up with a new plenum similar to the old one.
It will connect "A" to "B",, but it will not follow any rules of plenum construction.
That is my problem, in a nutshell,,,