If you check the guides, there are several gem recipes, and a couple ways of upgrading those gems.
Thunderrider, it appears to me, is trying to come up with an even better starting gem recipe than the ones psorek posted in his end-game guide, or that he developed and didn't really publish too well, such as the one found here : https://gist.github.com/quinor/2a554a9373987174269b
Right now, there are five, I think, different methods for upgrading a gem. From simplest to most complicated (which, generally also means least to most effective and least to most costly) they are the U method, the "weaving" or "spec" method, the 16 gem upgrade, the 64 gem upgrade, and the 1024 gem upgrade. Those three upgrades, by the way, were also found by psorek.
The U method is just that - taking a gem and upgrading it by hitting the letter U. This can be done more mechanically by duplicating the gem and then combining the original with the duplicate.
The "weaving" or "spec" method is primarily meant for emphasizing two colors in a multi-color gem. Since you generally want to emphasize the Black/White, and the Orange/Yellow, in a gem (depending on what the exact gem is) you would first Duplicate the starting gem, then create two more gems, one for each of the two colors you want to improve, at the same Grade as the starting gem. Combine one Single gem with the duplicate of the starting gem, and then combine the other Single gem with the original starting gem. Combine the two resulting gems.
The 16, 64, and 1024 gem upgrade plans were discovered by psorek. He's got both his 16 and 64 gem upgrades in his guide, I believe. He never really made the 1024 gem upgrade well known, because though it is more effective than the other upgrades, it is FAR more costly, and incredibly cumbersome to implement. There are a couple people who attempted to write scripts to do the 1024 gem upgrade, and those take some five minutes, minimum, to run.
The 64 gem upgrade plan is generally regarded as the most cost-effective means of upgrading a gem. You should be (barring the discovery of anything more effective, yet less cumbersome than the 1024 gem plan) using the 64 gem plan for anything you are upgrading, provided you are far enough along to find more than straight up U upgrading useful and not cost-prohibitive.