All batteries I’ve tried with the bike have been shorai lithium ion batteries.
The condition I pulled the 13.14v was with all running lights on, and no headlight. I’m just trying to get some form of charging before introducing more load. As of right now it’s not circulating any power back to the battery at all.
Have you noted the battery voltage change with RPM? What RPM does the voltage begin to increase?
The working voltage of a LiFePO4 battery, 4 cell (in series) pack is 12.0 to 13.2V.
An instantaneous battery voltage reading tells you nothing about the charging system unless you look at voltage change trend data. If the battery is under load, the voltage will show a depleting trend. If charging, the battery will show an increasing trend. The battery charge state dominates the system voltage. The bike can discharge the battery at a 10 amp rate without alternator output. (way more when the estart is used). But, a 12 amp alternator can, at max, charge the battery at a 2 amp rate and is usually lower at 1 amp while that 10 amp load is present. At idle RPM, a good alternator can only make 1/3 of is 5000 RPM rating or about 4-5 amps. At idle, your battery will deplete with the key switch on and alternator spinning. It will only restore power to the battery when the alternator spins fast enough to overcome whatever electrical load your bike has.
Your charging system should limit the LiFePO4 battery max voltage to 14.1 Volts, in order to treat it well. Charge controllers for lead acid limit to 14.5 V, which is technically abuse for a LiFePO4 battery. Also, for maximum LiFePO4 battery life, the voltage should never be allowed to fall lower than 9-10V, or damage can occur. Lead acid batteries can usually recover when severely depleted. It's a gamble for LiFePO4 tech about it's survival when overly discharged. Just note that three abused LiFePO4 batteries may all be damaged. Or, maybe not. It's not just voltage that determines a batteries health. It is voltage held while under full load that is the determining factor. A damaged battery may not supply full voltage under rated load.
While in the Navy, our parts stock room guy decided to test 1/10 amp fuses with a VOM in common use of the day. He went through a whole box of testing and declared all his stock bad. Sure enough, they were. His meter supplied 1/5 of an amp during each test blowing every fuse he had in stock while he tested them. Sometimes you need to use your head more often than a test tool.
Cheers,