If the car passed the E-Test the two previous years, followed by failing this year, with the same tune - the E-Test failure is not tune related.
Given that the car is predominantly stored (not used) the mileage since the last service / tune up is not that relevant. Store vehicles are often more susceptible to moisture / corrosion issues.
Start by checking for vacuum leaks and confirm consistent fuel pressure. Inspect the distributor cap and rotor, and change the oil and filter. It is a good idea to also replace the oxygen sensor.
A compression and leak down test will help rule out stuck piston rings, and / or a valve that is not fully seating / sealing.
If after all of these tests / checks, the vehicle still fails emissions, there is a very good chance that the catalytic converter(s) is the cause. Aftermarket cats won't last nearly as long as the OEM cats will.
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