what are the codes? a fuel injector doesn't "misfire" it either doesn't give gas, or it doesn't stop giving gas.

i'm not sure how you could not have a problem and do a Idle control sensor only to end up with these particular new problems. but based on the transmission codes, and a misfire I would say you need to start with wires and probably a coil pack. The burning smell could be oil in the spark plug valley, so you might want to do the valve cover gasket and plugs too.