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
PMK you are 100% right with everything you said. Get saddle height and peddle to spindle fit right first then dile in the handlebars and reach and it is not possible all he time to match bike to bike perfect. Also your right about tandems being diffrent even my tandems differ a little between each other due to each manufactures diffrences in build geometry.. That is why it is so important to fit each bike by it self and follow a good fit procedure step by step on each cycle based on its own specific geometry and your body.
The fit procedure I sent on a link above from Colorado Cyclist is a good one for example and I think the original poster should start from scratch and get it right based on his tandems specific geometry and not try so much to copy his single bike. I think he will be happier and get a better result this way.
NOTE not to offend here but that is what I have been trying to say to him but he keeps coming back and saying he is going to keep moving that saddle around to get things right trying so hard to copy his single bikes measuements exactly to a tee and maybe not realizing the seat tube angles and geometry of his tandem is more than likely way diffrent than his single. All this plays a big part into proper bike fit, more than most guys even realize.
That is why they have these fit procedures and if you follow them on each bike specific to each bikes specific geometry you can get pretty much the same fit bike to bike if done right and have your body fit right even though the specific measurements from bike to bike may differ.
Ride Safe All,
Bill G