My TR hasn't had a decent drive in about 2 years. Unfortunately when I started her up the check engine light is on, very high idling resulting in crunching into gears and fumes are very bad.

Anyone have any suggestions on these? any help appreciated.

Check the error code. With the ignition on, the diagnosis connector will output codes constantly. Its easiest to check codes with a 12v LED light.

https://www.dropbox.com/s/ofkqwpza31uca3s/error%20codes.png

probably suffering from lack of use.
Just take it for a drive!!
rumpfy

Gotta agree with the above, take it for a drive somewhere for about an hour or so, dont put your foot down until the engines warm, but keep the drive moderate just to get the car adjusted to something other then sitting around for 2 years.

You cant expect a car that's been sitting around for 2 years to be like new when started up, seals dry out, coolant dries up, engine parts seize, its just something that time does to a car.

And get fresh fuel?