New Heat Pump - York or Trane?

I'm looking for a little advice. I need to replace my HP and have two quotes so far. The unit will serve the 2nd floor and a small finished 3rd floor area, total size of about 1,900 square feet (300 of which is the 3rd floor). The old unit is a 20-year old 2.5-ton 9 SEER Trane model. I live in Virginia and the current unit has serious trouble keeping up during the extreme (for our area) hot and cold temps, below 30 or so and above 95, which is probably only a potential issue 2-3 months total out of the year. I also realize that a HP can only do so much once it gets real cold.
First quote is for a York LX (YHJD36S41S4 (3 TON) 14.5 SEER / 12.0 EER / 8.2 HSPF heat pump condenser unit) with a York air handler (AHE36C3XH21 air handler with 10 K.W. heat package). This is from a reputable, decent size local company that includes a 10-year labor warranty on top of the 10-yr parts and compressor warranty. Total price with install is $5,500.
Second quote is for a Trane 14 SEER 3.5 ton unit and 3.5 ton air handler - don't have the model # on that one unfortunately. This is through a "side guy" whose full time job is installing for a larger company and he does this on the side. Total price with install is $4,850.
Realizing that a correct installation is most important I feel like its a no-brainer to go with the reputable company. Plus they have the good warranty. That said, is the York model significantly inferior to the Trane? Is there any chance that the Trane unit would be sufficiently better (quality and size-3 ton vs 3.5 ton) to warrant going that direction to also save a few hundred bucks?
Also, both of these would include flushing the existing line set rather than installing a new one. Any reason I should be skeptical of doing that? To add a new one would add a good bit to the price and there really isn't a good place to put it on the outside of my house due to multiple roof lines.
Any advice would be greatly appreciated!
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