You have a problem with your cabling Mike. 17v is too high really.
for the 50 A unit, 25 mm2 is adequate, for the 110, 35 as a minimum, I use 50mm2 on a balmar 130. with SHORT runs.. you say you have a lot of cable length ? if so, definitely 50mm2.

a lot of your problem, knowing the voltage now (And presuming that is AT THE ALTERNATOR - not at the batteries !) then the cabling is inadequate.
The diode splitter will drop 0.6 to 1v. easilly made up at the alternator. I would aim for a max voltage at the alternator of 16v. assuming 14.8 max at the batteries i(f wet cell)

The other thing to consider, is how are you reading the output current - with a splitter you have two banks, are you monitoring just one, or both ?.

Max recommended size of alternator on a single belt is 130 Ah.

the output from the alternater to a disharged bank (Assuming a 110 unit and proper cabling - ) should peak up to 90 amps for a short period (You will very rarely if ever get the maximum due to heat and the fact the alternator was not designed for marine use - ie, a higher voltage than automotive and much more use)

My 130ah alt can peak at 115 for short periods - that is controlled by a balmar reg also.

The stirling unit should not need any adjustment - afaik the dip swiches are only for the battery bank TYPE. there is also a fuse that can be fitted in two positions for either neg or pos field reg alternators.

No problem on the switch, there are deatails in the stirling reg manual afaik.

Hope that helps..
I would firstly change to 50mm2 cable, keep the runs as short as possible. try the older alternator first.. the cable will be oversized a tad for your existing alt, but thats better than undersized and allows you to go up in size on the alternator without changing calbing again.

Hope that helps Mike.

Ps Charles Stirlings instruction re voltage drop and cabling are very comprehensive (Assuming the pro digital unirt) - have a browse through that as well.

Cheers n beers

Joe