[replicat]

Setting first mudra to true = dps loss (even if its just 0.x% dps) since the bot waits for the next spell to be used, before casting mudra. (nope, its not casting mudra if mudras get rdy while being in a gcd)
Setting first mudra to false = the bot instantly uses mudra as soon as it gets ready without waiting for the next spell to be casted.

And for the loop thing, I found another solution, i think. (Missing Mudra Buff got nothing to do with the loop thing.)

Although I believe that GCDs come in precedence before mudra when oGCD time < 0.5 (for Raiton) and 1.0 (for Suiton) as mudra chain have a way longer casting time, I have not tested it thoroughly so I am in no position to make any statement regarding the DPS loss. It is a balance between delaying GCDs and delaying the ninjutsu CD.
I may try conducting some research on the GCD/Mudra thing... _(:3 」∠ )_

If yours is the case then you may try filling the 'Previous skill ID Not' of all first mudras with all of the ninjutsu skill ID and see how that worked out. That should prevent any loop on failed cast.
And I wonder what is your solution to this? I am always curious about alternatives.