I bet it felt good to drive it after so much time, money and ones heart into the project.

Heartbreaking though to have a serious leak as you have. I for one do not like the pan gaskets for these. I only use the Grey sealant for the non gasket joints. Good luck can be had with the Black but any of the other styles have not been as reliable from what I have seen.

Oil, Look in your front cover first. You should be able to determine if it is the seal or pan joint, hopefully it is the joint but be prepared to deal with the seals. I do not use repair sleeves very often, I thought they were the greatest thing when they were introduced and have had some great success with them. But there is so much that can go wrong too. There is a good chance the lip of the seal might have tripped when assembling them. This can dump the spring out of the seal.
Personally I prefer to move the seal in or out to get it out of the worn groove before I will use another sleeve again. I really will only resort to using repair sleeves if the surface is pitted.
I have removed sleeves in the past.

Tune, consider what the autotune did to be where that region needs to go. If it added fuel to an area go ahead and bring up the surrounding bins. Likewise if it leaned some. I burn and save after every pull.

If there is one real big benefit to the MS2 processor is stability. The earlier processor would suffer resets and was very prone to corruption. The main reason for saving a session. I have been on the road and the engine would just backfire and die while driving. You would sit on the side of the road reloading the firmware and then the MSQ hoping the plugs were not so fouled that it would not fire up again. This seems to be gone now.