Who told you the bike was lean at 13.1? Ideal Stoichiometry is supposed to be at 14:7.
The only way I've ever found to do a mixture check other than sniffing the smoke pipes is to install a new set of plugs, run it through the gears wide open. Shut it off with no idling, and pull the plugs. Then read them.
With a carburated bike you can't get an accurate picture of the mixture ratio unless it's up on the mains, at WOT. The dyno guys should have a sniffer going while your bike is running on it.
Why did you jump from what you say is really lean jetting to really rich jetting? In drag racing cars anyway Holley recommends coming up two jet sizes per jet change until you get too rich then go down until it makes the most power.
I would also recommend just changing one thing at a time. Do the jets and get them squared away, then play with the timing but not at the same time.
Maybe you've done all of this, but it all comes back to doing the basics when one gets lost, and believe me, I've been there.