I have a 40 year old 1200sqft raised ranch in SE PA (hot/cold climate). in my well vented attic that has plywood installed for storage, I recently installed a new ac unit with wrapped metal ductwork and then flex duct to the registers below. I noticed two problems this past winter, 1. the ductwork was condensing a lot of water inside during the cold months. 2. I noticed what appeared to be, dare I say, mold on the underside of the plywood. I have a minimum of 6” of insulation under the plywood. Would it be easier to insulate the rafters and just turn this whole attic space into a partially conditioned space? Or do I raise the floor add more insulation to the floor and duct?

The AC ducts should not condensate at all. If they are the vapor barrier used on the insulation was not sealed properly. If the ducts were condensating on the inside in the winter, you need to control the amount of moisture in the home.

The vapor barrier in the attic is either not esistant or in very poor shape. In any case you need to remove the old six inch insulation and replace it with attic blankets with a vapor barrier facing towards the inside of the home. This will not stop the moisture entirely but will slow it down considerably. In addition the plywood flooing is trapping the vapor. You need to allow for ventilation between it and the top of the insulation to allow the attic vent system to remove the moisture that excapes through the ceilings.

So raise the floor. Install new thicker insul to save money. Then when replacing the floor allow for air to freely travel under and out of attic. Ideally the attic temps should be as close to the outside temps to prevent ice damming, and longer roof life. BE sure to drain the condensate trap in the attic so it does not freeze and crack causing a leak when you use it next year.
You can shut off the ceiling grills to help prevent any interior condesate as well. But making sure the insulation is on the ducts and sealed you should be fine in that regard.

Pennsylvania Energy Code requires a minimum of R-38 in the attic for most parts of the state.

This equates to about 14" of insulation in any attic floor.

Pennsylvania Energy Code also requires any ducts that are installed in an 'unconditioned space'...such as in an attic outside of any heated or cooled space...to be insulated to at least an R-8.
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Sounds to me from your description that your ducts are not insulated to code minimums nor is your attic floor.

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While 'conditioning' the attic, by insulating rafters, blockings all vents, and heating and the cooling this space is one approach....It is the most EXPENSIVE approach....and may not yield any actual savings for 20 years or more.

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Best to increase duct and attic floor insulation...and stop all air infiltration between the attic a nd floors below for best energy and dollar savings results.

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Least costly solution:

-Add insulation to give you at least R-38 in the attic ceiling

-Insulate ducts to at least R-8 or more