No Start, ignition and ammeter problems
By hooking to the alternator output, you are "backfeeding" from the alternator, through the bulkhead connector, and to the factory splice in that wire just before it gets to the ammeter.
Suspects are
fuse link
bulkhead connector problems
bad connections at the ammeter
bad ammeter
Read this excellent article which, even if you don't do the bypass they are suggesting, this article gives a good overview of problems with these cars, AND a simplified wiring diagram of the area of concern:
http://www.madelectrical.com/electricaltech/amp-gauges.shtml
You can download a complete service manual for free from MyMopar. Only problem is you'll have to "play" with page numbers, because they are not using the Mopar "dash" numbering:
http://www.mymopar.com/downloads/servicemanuals/1966_Plymouth_Service_Manual.zip
Also from MyMopar are useable wiring diagrams. These are not always correct or complete, but they are sometimes easier to follow than the factory diagrams
http://www.mymopar.com/downloads/1966/66DartA.jpg
http://www.mymopar.com/downloads/1966/66DartB.jpg
On diagram "B" above, near the top left, find the starter relay, "dark blue tr" going up to "Z" of the bulkhead connector.
The second connector to the left, RED coming off of "Z" represents the interior half of the connector. Go to diagram A
About the 13th wire down from the top on right side of page is this same RED, and if you follow it you'll see it goes directly to the ammeter
Somehow, you have lost power to this wire, OR the ammeter is bad/ bad connections, and is breaking the circuit.
In the factory manual you can download, the electrical (page 8-1 marked on the page) begins with about page 189 of your viewer
The wiring diagram index, 8-101, is viewer page 289
Your engine bay diagram, 8-118, is viewer page 306
These older diagrams do not have the wire colors encoded into the wire number. You must use the chart on the side of the page.
Find the starter relay, top left of page, and come off the bottom stud angled down and then to the right, you'll see it's labeled "fusible link" and is labled wire "A1B" and goes to "Z" of the bulkhead connector. The chart on the side of the page shows "A1B" is a no16, dark blue with tracer
Also just down from the top and to the right is a diagram of your bulkhead connector, as viewed from the engine side. Check out the connections in there carefully, as this is your NUMBA ONE suspect
For the "rest of the story" (instrument panel diagram) we need 8-114 and 115, viewer page 302
Find the bulkhead connector at about middle left of that page, and Z (A1) goes up to the right and off the page, to be continued on next page down
On page 303, "A1" comes back on the page about 16 conductors from the top of the page. Follow it to the right and you'll see it goes right to the ammeter. If you look at the chart on the right, "A1" is now a no 12 RED.