Personally, I'd replace the system. A new a/c could be twice as efficient as the old one. The furnace could be in the low-90% range, probably 20-40% more efficient. Not sure what your utility bills are, but they are unlikely to go anywhere but up.
One thing I really like on my (also Trane) system, is the variable speed fan option. It allows you to extract much more moisture out during the summer and the start and stop are almost unnoticable because of the ramp up/down funtion. In the winter, you don't get that short blast of cold air when it first starts up until the air in the ducts gets hot. It also runs after the a/c or heat is on to extract the conditioned air you've paid for. Couple the dual-stage furnace with the variable speed fan and expect nice, even heat or cooling with good dehumidifcation. Since it does so well on dehumidification, you might find you are comfortable at a higher temp, saving even more money.
Technically, the a/c people should not have added refrigerant without checking for leaks, if I understand the regulations.
The new refrigerants are less detrimental to the environment, too.
Check with the utility company to see if any rebates are available...I had a new boiler and WH installed and got back $1100.