Read the section in EGV107 about setting the Throttle Position Switch (TPS). Make sure it is set properly so that it will signal to the ECU that you are at idle. You should be able to set knob in middle or range and fine tune idle mixture by going a click at a time followed by short burst of throttle.
Resistance testing of MPS is covered in the shop manual. Also check with Mityvac or similar that it will hold say 20" of vac for 15-30min. To test if it is working properly and make adjustments, you need an exhaust analyzer or a wide band AFR meter (I could never get my car right until I installed an AFR meter, but hardly anyone here has one!)
Probably not your problem, but you can immerse the injectors in carb cleaner. There are small screens on the inlets. You can remove those for cleaning by screwing in a suitable sheetmetal screw and pulling to extract. I set up a kind of crude system to flow test the injectors using my pressure brake bleeder. I think it is in the Comprehensive guide in the stickies. Later, I did 4 at a time using spare fuel rails and compared the amounts collected. At first I used Seafoam to clean, then carb cleaner. For flow testing I used clear mineral spirits/Varsol (not gasoline!)
Don't know why you are getting misfires. Usually timing or ignition problem. Follow what Cush said and get things in good shape firts (Sounds like you are well on your way). Pertronix eliminates points as a potential problem - covered in Stickies. Make sure rotor and cap are aligned. Check for damage to contacts in cap.