Pretty much the ideas posted are valid. As mentioned, I would prefer to see a good fit of seat height, seat fore aft relative to the bb and then dial in stem length.

As for where you place the eccentric, fore vs aft, above vs below center, this all is a matter of you and your stoker as a combined fit on the bicycle.

Aim for, but don't get too wrapped around the idea of an exact same fit as your single bike. For us this doesn't always work. The tandem rides different, often does not see the riders stand as often, and for the captain requires different amounts of strength vs the single to maintain control.

My recommendation, as much as you are worried about your fit, get the back seat perfect first. If not you WILL need every bit of efficiency to go fast as your stoker becomes uncomfortable.

Get the stoker the best fit for long term seated pedaling at her cadence. Suffer a few rides to ensure this. THEN, knowing the exact parameters of the stoker, start working on fit for the captain. Obviously, get the seat height and fore aft dialed in first. If this means moving the eccentric do it. Work the bars position as a final chapter.

In regards to stability, CG, and so forth related to the eccentric, these all relate to control, but a good fit easily knocks eccentric position to a distant second. If you need a reason to run above center, tell other teams it is for better clearance when hammering corners leaned over and pedaling.

FWIW, my so called stumpy legs on my 5'10" body and a 5'6" stoker have had the eccentric on all our tandems, both past and current run the eccentric above center and forward.

Be patient and best of luck with it. I would be very surprised if your best overall fit for captain and stoker was exactly as it would be on a single bike.

BTW, regarding the brakes, make certain they are properly aligned and the discs have been cleaned with solvent, then with a reasonably weighted rear seat, burn the brakes in with some serious hard stops. Your complaint is typical. They should get much better.

In regards to the cables and other oem fit of stuff. Remember the bike is a production machine and not custom built and assembled. Get all your fits and such dialed, then have the shop build it right in your eyes. Shortening new cable housings are easy and inexpensive. Regarding the brakes it will also make them more solid at the lever.

PK