I doubt your problem is valve train. This is more typically due to an injection pump problem, however it could also be injectors. The smart way to approach it would be to get your injectors tested, and if they are good, then get a pump. But I can tell you that your injectors will not likely be perfect, and the money spent to test them at 45,000 miles is a poor investment, since IF they do find a bad one or two, and you choose to replace it, you will be out the cost of injectors and a return line kit. The best return on investment with these trucks any time there is a fuel system issue, is a new pump and injectors all at once. That way, you get your 100K out of a matched system, and it doesn't spend the next decade nickle and dime-ing you to death.
Any time you turn up your fuel, you do divert fuel away from the advance circuit, retarding it slightly. You could try activating the cold advance with an alligator lead and running it that way to see if your problem goes away.