You were right to bring up your concerns. With a J load calculation of 72,000 BTU, even though a 96% efficiency 80,000 BTU furnace could be considered slightly oversized it would most likely have been a better choice.
That being said, if you have a local HVAC contractor you trust and can come and do a proper site/equipment inspection there might be a couple of simple adjustments that can be made with this new installation to help a little:
sometimes even a swap of what filters are being used can make a difference - In older homes and ductwork designs, a higher MERV rated filter can be detrimental to the needed airflow with unnecessary restriction. I normally recommend a MERV 8 pleated filter where this is a concern.
There could also be an issue with with how the furnace was initially set up to jump from 1st stage heating to 2nd stage heating - I was at a service call recently because a homeowner had said that a newly installed furnace was not keeping up and he needed a second opinion. It turns out, that the furnace settings, by default, would require that the thermostat should be set-up to determine when 2nd stage heating would kick-in. However, because the thermostat was only wired for single stage communication, a simple setting on the furnace needed to be adjusted to allow the furnace itself to initiate the second stage of heating after 10 minutes - otherwise the furnace would only ever run on the single stage heating, never stopping on colder days as it could never reach the desired temperature because of a significantly reduced heating output.
For that Trane model - if the thermostat is only wired to the the one heating terminal (w1) on the furnace control board and is not set for 2 stage communication with it also being wired to W2 and the thermostat settings adjusted to 2 stage heating needs - the furnace will only run on 1st stage heating unless the W1 and W2 terminals are jumped together at the furnace board allowing the furnace itself to initiate 2nd stage heating after a set-time.
If your Trane is only ever running on 1st stage heating, then your 60,000 BTU furnace will only run at about 38,000 BTU's
I hope this helps