It would be helpful if you posted the model numbers of the equipment in your quotes. You can also post the prices if you want comments but be aware prices vary by location.

Is the basement 900 sq. feet? If yes then a 2 ton unit seems is very over sized.It does not take much to cool a basement if it mostly underground. My suggestion would not to spend money on a 2-stage unit and buy a dehumidifier. You could be the $300 big box store 70 pint type, but in your case you may want to spend the money on a better unit such as a Santa Fe brand. It is three times the prices but will last a long time and dry out your basement.

Seems a bit steep, even for Trane. A simple, bottom of the line, 13 SEER, 1.5 ton, replacement installation typically runs half that (Rheem, Goodman, Carrier). Going up to 15 SEER and a VS air handler should add less than $1000. You probably only need a 1.5 ton outdoor unit. But a 2 ton variable speed air handler (which is probably the smallest variable speed air handler they make) will dehumidify better than a fixed speed unit. A Variable Speed air handler will run about $300-$500 more than a fixed speed, depending on how many additional bells and whistles it has.