I had a problem with my TDi going into Limp Mode. Similar to yours but in a diesel. I replaced all vacuum lines, the actuator and even some of the relays and got nothing, so I know your pain. One other thing to consider, and may sound odd, is the cat. If it gets clogged it will cause too much back pressure problems as well. Too much back pressure might cause the backfire through the intake as the exhaust has no where to go. I could be wrong, but being an older car, it may be this.
I never fixed mine completely lol, but still averaged 48-50mpg, so I quit trying. Spent too much money on a car with 350k miles on it.