Motor is running crappy after check engine light comes on, Any Ideas?

The carbon canister connects to a vacuum line in the front of the stock upper manifold. A lean condition may occur when it is disconnected since it vents fumes from the gas tank into the intake manifold. If is disconnected, make sure the vacuum line for it is plugged at the manifold.

If after checking the system for vacuum leaks using a vacuum gauge and getting at least 16 inches of vacuum, suspect the O2 sensors. They are only supposedly good for 60 K miles.

Here's the tech note for codes 41 & 91

Code 41 or 91 - O2 indicates system lean. Look for a vacuum leak or failing O2 sensor.
The computer sees a lean mixture signal coming from the O2 sensors and tries to compensate by adding more fuel.

Measuring the O2 sensor voltage at the computer will give you a good idea of how well they are working. The computer pins are 29 (LH O2 with a dark green/pink wire) and 43 (RH O2 with a dark blue/pink wire). Use the ground next to the computer to ground the voltmeter.
The O2 sensor ground is in the wiring harness for the fuel injection wiring. I grounded mine to one of the intake manifold bolts

"When the mixture is lean, the exhaust gas has oxygen, about the same amount as the ambient air. So the sensor will generate less than 400 Millivolts. Remember lean = less voltage.

" When the mixture is rich, there's less oxygen in the exhaust than in the ambient air , so voltage is generated between the two sides of the tip. The voltage is greater than 600 millivolts. Remember rich = more voltage.

Here's a tip: the newer the sensor, the more the voltage changes, swinging from as low as 0.1 volt to as much as 0.9 volt. As an oxygen sensor ages, the voltage changes get smaller and slower - the voltage change lags behind the change in exhaust gas oxygen.

Because the oxygen sensor generates its own voltage, never apply voltage and never measure resistance of the sensor circuit. To measure voltage signals, use an analog voltmeter with a high input impedance, at least 10 megohms. Remember, a digital voltmeter will average a changing voltage."
Charles O. Probst, Ford fuel Injection & Electronic Engine control

I recommend that you get a copy of the Probst book if you plan to keep the car and do your own mechanic work.

Ford Fuel Injection & Electronic Engine Control 1988-1993 by James Probst :ISBN 0-8376-0301-3.

It's about $20 from Borders.com see http://www.amazon.com/ . Select boo...very good, and I found it to be very helpful.