This is really weird becuase the valves tick when hot. Most times your valves will tick when cold and you will run ruff. I am not trying to say that it is a valve tick, but are sure that that is exactly what the sound is. If I were you I would go to an auto parts store and purchase a mechanics stethescope. Use this on your valve cover when you think the valve tick is happening. It could prove to not even be that. Another thing, this is kinda out there but are you sure that your injectors are good? If a cylinder isn't getting gas then you will have a problem. It also seems that it may very well be a electrical problem. Once again this is out there but it seems that you aren't having any luck so...it may be that your motortronic is the problem. During use a computer will warm up. some how you may have a problem in your motortronic that causes this noise and the rough running. Try switching your focus to electrical problems. something like this always seems to be easily overlooked. sorry for the stupidity.