[Step 0] Neck setup After stringing by replacing each string at a time, do a rough tuning pass E -> E,a -> E,a,d -> and so on Check neck is straight, make sure the nut is unlocked then loosen the strings a bit, follow that with adjustments to truss rod. Retune roughly and lock at the nut play the guitar a bit, do some whammy bar pulls and dips to stretch the strings a bit

[Step 1] Initial Tuning Tune (without locking at the nut) [tune like this: E, e, B, A, G, D] No nut locking here because the rest of the adjustment will have it go out of tune anyway. Also make sure that the adjustable micro-tuners at the bridge are mid-way before starting the tuning process.

[Step 2] Bridge Leveling Adjust the bridge level, have it sitting back a tiny bit, because once locked at the nut and re-tuned, the strings will pull it back level. If the bridge is sitting back too much loosen the claw screws, if the bridge is dipping forward too much tighten the claw screws. Make sure to do 1/4-1/8 turns at a time.

[Step 3] Tuning Tune (lock at the nut) [tune like this: E, e, B, A, G, D] Now check that bridge is nice and flat with the body, if not unlock then repeat Step 2 and Step 3

[Step 4] Action I aim for 1.7-2.0mm on the low E and 1.5-1.7mm on the high e. (I'm using Hybrid Slinky 9-46) Unlock the nut, chock the trem with something like a strap or a piece of cloth, and lower/heighten the bridge depending on if action is too high or too low. After adjusting bridge height, tune, lock the nut and check for action and bridge level. Fixing level first if its off (Step 2), then back to action (Step 4)

[Step 5] Intonation Unlock at the nut. Do this for each string [intonate like this: E, e, B, A, G, D] If the 12th harmonic is flat: chock the trem, loosen the string, shorten the string length by moving the saddle towards the neck. If the 12th harmonic is sharp: chock the trem, loosen the string, increase the string length by moving the saddle towards the bridge. After each adjustment of each saddle, unchocking the trem and re-tuning of the entire guitar is necessary. Once in tune, move on the next string and repeat the process until all 6 are properly intonated.

[Step 6] Final tuning Tune the guitar and lock at the nut. Check level and action and make no more than tiny adjustments if necessary, if it feels like more adjustment is required, go back to the respective step.