I also got the mod2 upgrade at the same time as I fixed power supply issues. It's a different camera - works so much better after the repair and the modifications are lovely. The big one for me is the AF offset which adjusts itself automatically when changing AF lenses - and it is SO accurate. I have been photographing bees collecting nectar with the AF 180 + 1.4 x + extension tubes and was shocked to see how easy it is to use the nominal aperture of 2.8 and get crisp focus with the leaf aptus 12 - you can see every hair on the bees.
I don't mean to imply that the AF can track the bees with that extreme telephoto and macro, but I do use it to get a quick focus on a petal or stem and then follow the bees manually.
I spent a solid day in the studio using a bar code sticker to adjust the focus offset of each lens. the camera was tethered so I saw the results pretty quick. For each lens, I tried a series of close and mid-distance shots using the AF or focus confirmation and then used the results to determine the best focus offset for each lens. It did take a while and it was a pain, but you have to do it just once. I stuck a little sticker on each lens with the correct number, but as I said, for AF lenses it is set automatically.
This is one heck of a system, it is just a pleasure and so exquisitely precise. There are occasional hiccups on the electronics, which are annoying, but I shot hundreds of frames today.
You'll work through this, no problem, just a little time.