Hi Mike,
Figure the water Line being very close to where your bottom paint meets the Gel cote or where the bottom gel cote white stripe is (if you have that like mine does).
I set mine up so that when the motor bracket was at its mid setting (like you see in my album) the cavitation plate would be a few inches below the perceived water line. That way i could let it down further if needed under choppy conditions. I leaned towards having the motor able to go lower than is most likely needed but this takes away from being able to get the motor up and out of the water when at rest. You'll have to make that decision on your own.
I have not got the boat in the water as of yet so i cant answer any questions on how it performs but hopefully very soon in next month or 2. No matter how low the motor is capable of dropping I anticipate that it will come out of the water under the right conditions, however; under those conditions i expect to be under sail 99% of the time.
For placement off center line, I dont think it matters much, I placed mine as close to center line as I could. My ladder is off to the port side so all i needed to do was ensure i missed the cockpit drain structure with the mount bolts. I haven't posted pics but I've added a secondary motor mount off to the starboard for an electric trolling motor ( I like backup systems).
Some guys mount their motor brackets direct to the transom which i guess works great. I preferred to sandwich the transom between 2 pieces of star board (inside and outside). I think it adds support as well as a cleaner look and i would suggest you do the same. I also used 5200 sealant between star board and transom both inside and outside). Make sure you mask everything off before mounting with the 5200 keeps you from getting that nasty stuff all over.
As for my inboard tank, No, i dont have any issues with the fuel pump pulling up from the tank through the water seperator. I did however rebuild my fuel pump because I was afraid of same thing.
Please ask any further questions you need to. I'll keep an eye open for your replies.
PS, when you do mount get a second hand to help. it makes it a lot easier holding everything in place when your bolting down.
Good luck and thanks for asking