Nice Canondale, it looks great,
Some of the issues you mentioned is why I build my own tandems. I have them dilivered unasembled from Co Motion & da Vinci but with the Canondale that is not an option. When we purchased the Cannondale we use to own I disasembled it down to the bare frame and built it back up correcting all the issues such as cables being to long and adjusted everything to spec includeing all our documented fit specs/measurements for proper fit.
You mentioned moving your seat back to get fit correct. I suggest to you before you do that check top tube length between your single bike and your tandem (I bet the tandem is longer) and make sure your knee to peddle spindle measurement is correct. If your still to stretched out more than likely your top tube is longer on the tandem than your single and you will need a shorter stem on the tandem to get things correct. This is the proper way to adjust your reach instead of moving the saddle back or forward. Always set saddle height and knee geometry to peddle spindle first (with plum bob as mention above) before adjusting reach to bars and do not use moving the saddle back and forth for this adjustment. Always adjust the reach to bars with the length of stem used to get your reach to the bars right. (the rule of thumb is the bars should block out the front axle or hub when riding on the hoods if you glance down)
You mentioned the stoker bars hitting your hips that is why me and the wife swithed to the set up below to solve the issues that are commen with regular 44cm/46cm bull horn stoker bars that come on tandems new.
(NOTE COPY OF POST BELLOW) sent in another thread explaining the stoker bar configuration we changed to to solve the issue your having with your hips hitting the stoker bar.
The stoker bar is a 50 mm rise x 29.5" 31.8 clamp mountain bike downhill bar ( the exact bar is is a Funn Fatboy bar cost $44.00 the grips are Ergon GS3 leichtbau composite size small $54.00) both purched at Universal Cycles online.
The bars have bean cut down to 22" or 55.8 mm wide ( would not recommend cuting shorter) I cut 3.75" of each end with a tubeing cutter (nice clean cut). They look really short after you cut them but as you can see on the tandem they turn out just fine and are wider than the captains bars leaving plenty of room still for your hips. I have run this type of bar with diffrent grip styles on all our tadems my wife and stoker loves them. Any brand moutain bike riser bar will do the job just pick the amout of rise you want 30 mm, 40 mm, 50 mm some times they say 1", 1 1/2" or 2" rise have even seen 3" rise offered. I like them better than any of the 44 mm or 46 mm wide stoker bull horn design bars that come on tandems myself. The moutain bike riser bar cut down is wider and more comfy for the stoker.
See Pic's below of our Co Motions we have owned & our new da Vinci Joint Venture with the stoker bar changed to a cut down flat bar set up. The Co Motions are cut down to 22" or 55.8 mm but with a 40 mm 1 1/2" rise instead of the 50 mm 2" rise like on the da Vinci. I put a 50 mm or 2" on the da Vinci because they worked out better with the type of stoker stem that's on the da Vinci to get the stokers fit where she likes it..
Ride Safe ,

Bill G