What kind of injectors did you put in? Also, you might want to check your plugs, should be NGK. The best $20 you can spend is for the Engine Temp Sensor, simple to change and you know it'll be working properly. How many miles on the o2's? They might be reading lean and not changing due to a fuel related issue - the injectors. WHen you said whole side of the motor wasn't running that could also be PTU issues. Check all connections in the engine bay for corrosion.