Given the questions you're asking, it seems to me that you just jumped into ID abuse without having done other simpler RNG abuse first. If you had done other stuff, you'd probably be able to answer most of your questions yourself, particularly in regards to Timer0. Have you at least read the guides posted in the first couple posts of the Gen 5 thread?
The simple answer is that Timer0 is a value taken from your DS's hardware, and it's not really controllable. But you should be able to hit both of your values via trial and error.
Do you mean frame 43, or are you talking about a different ID frame now?
If you're not getting a recognizable string of natures, the most likely reason is due to the Timer0 value changing on you. It will unfortunately require more attempts at hitting your seed (this is the original flawless IV seed, not the seed you hit to get your trainer ID) until you can work it out. The problem with RNGing starters is that it's difficult to check IVs, but since you're going for a flawless spread, you should probably be able to tell if you hit it.
The ID frame and the shiny PID frame are not the same thing. Right now you are aiming for the ID frame, which is on frame 43.
Once you have hit your ID, save in front of the gift box. Then you need to restart and hit your seed for the IV/shiny PID (the first seed that you found with flawless IVs). Take the Tepig from the gift box, do the battles, and see what nature you got. Try to find that nature in the PID frame list for that seed, or in the PID frame list from the Trainer ID Searcher. Then you will know how many times you need to advance your PID frame to get your shiny. After that, reset and hit that seed again, and save as many times as you need to advance the PID frame. If you did everything correctly and hit the right Timer0, you should have your shiny flawless Jolly Tepig.