IMHO timing is not the issue. Over the years of owning the Jeep, masking problems becomes an issue. If the Jeep is put back to "Factory Specifications" it will run, and run well. However:
1. who the heck knows really how to do that?
2. And if they did could they really afford to accomplish the task?
So, the next best thing is here a tweek here, there tweek, everwhere a little tweek-tweek. With each tweek the owner puts the vehicle a little farther from vehicle specificaitons. The problem that necessatites the tweek has not been fixed. It's only been "worked-around" by the tweeking. Each time the Jeep runs a "little" better with no explination. Then one day all the tweeks cascade and the Jeep dies and the owner says: "But it was running so well, I don't understand what happened?" There is great truth to the statement. The owner really doesn't know!
So now you go and put on the TR upgrade and it's really a matter of two things:
1. Backing out of the "tweeking" that's been done over the years.
2. Perfoming new "tweeking" for what would be Spec. on the TR upgrade.
So, it boils down to is all this tweeking normal on most of the upgrades?
In a nutshell.... yes, it just depends upon what the defination of tweeking is.