Waiting for the frame to advance is the worst, what I do is max the speed on VBA and go into a battle, battles skip every other frame for me essentially doubling my speed, other than that there's really nothing I know of.
And you can use the seed the .lua script gives you to see how far away from your target you are, but that's still limited by RGN reporter's range, the only other thing I can think of is you could use the seed and generate the frame1 spread for it and search for that in an old version of PokeRNG (the one for 3rd gen).
You need to figure out what SID you need for your target to be shiny with the TID you get (there should be a range of 7 for the SID), there are a couple ways to do that but I use Pokegen to figure it out.
Next you copy your list of seeds to notepad and convert your highest and lowest wanted SIDs to hex, write those down somewhere, if they're 1111 and 1118 (example) you would search for (space)111 in the list of seeds and look for the next number to be between 1 and 8, if your hex is only 3 (or fewer) digits then add more spaces to the start (adding spaces ensures it only looks at the right part of the seeds).
If you can't find anything search more frames, when you do find it figure out which frame it is (can take some work to do it), then just advance, taking into account how long it takes to generate the SID.
Not really sure what you mean, there's really no reason not to just RNG your SID now, Hozu has a guide to it here.
And main window of RNG reporter can search 99,999,999 frames, any more than that and it's much faster to use the new game trick (check my convo with Lord Scalgon for info on that if you need it).
I didn't want to flood DMP with questions, but based on what you're saying, this is what you did:
1. Set the time and started first timer.
2. Started game when the first timer's first countdown ended.
3. Entered the game, checked to see if you hit Timer0 via Chatot. If you did, then you turned on C-gear.
4. Hit the Entralink button, waited in the "x entered the Entralink!" till first timer's second countdown ended. At this point, when you press A, you started second timer.
5. Advanced IV frame (if necessary), talked to target Poke, waited till second timer ended before battling Poke.