I don't read everything in this post, but question is where we need start?

Look in the corner down left.
Only one have something in the middle, and those give us where to start???
i mentioned that before as a possibility but it's wrong, look at the rabbit and he'll tell you where to start.
Does the repeating pattern in the heights still hold true if you start with that flame?
I believe that No, it does not. Alphabetcanary's pattern only works if you start from the top left inner flame (yellow and blue), work your way around clockwise. Where the inner pattern finishes, the outer pattern starts, only you need to move counterclockwise. Also, if we start counting where a-canary's pattern starts. Every 6th flame is a 0 (The entire way through). (I guess you could start with the outerflames, then work your way in.. E.G. Read the pattern backwards)
Alternatively. The pattern exists on its own in each track. If you aren't concerned with the pattern wrapping, then you can essentially find it wherever you want. (It just won't continue all the way around, unless you resort to reading the tracks completely out of order. (Meaning you will need to mix inside and outside tracks)
I mean, what does it matter where you start? The pattern exists on every second flame. There is no authority nor reasoning (at present, at least) telling if it should be
short-undefined-long-undefined-long-undefined
or
undefined-long-undefined-long-undefined-short
or
long-undefined-long-undefined-short-undefined
or so on, so on (and you can choose one of two directions, too).
I mean, you can start the pattern on a short flame, long flame or undefined flame. And there is no reason to assume that the pattern cannot be started on any arbitrary flame, as smracer asks.
The only tricky part is going from inner segments to outer segments and
vice versa - the only place preserving the pattern is at the top left corner