The F59PHi could work during the transition period between the Phase III and the Phase IV paint schemes. It is your railroad so run it how you want to!
I hear you on the Dash-9. 6 wheel trucks and a really long chassis for the 15" cars. The RK Genesis might work really well for you as it is sized more proportionately to the cars you have. Also the RK F40PH is just a little smaller than the Premier version. I somehow ended up with both RK and Premier F40s over the years. Another possibility is the K-Line F40PH. Outside of the sound system, I actually like them a little better then my MTH ones. There was one on the buy sell board today for a reasonable price.
The Atlas Dash-8 is correct but finding one is hard. An AEM7 is a great suggestion and I might I also offer that the Williams E60 is "right sized" for your 15" cars. They can be found often around $100. Nothing fancy, but not bad engines. I also have the Williams SD90 in the Pepsi Can scheme. Not correct in any sense of the word, but again a solid puller in a pinch when I'm running all day for the public.
While the Horizon Fleet did not run out of Boston, HEP equipped FL9s did pull Amfleet cars on contract commuter trains. Granted the Amtrak 3rd Rail FL9 is not an easy find as they only made 20 and I have 2 ... :-), However, a Phase III painted F7 might look good too as a stand in.
As for paint schemes for your cars locos in Phase III or Phase IV paint work just fine. There was quite a bit of overlap during that transition. I found a neat photo online of an E60 pulling phase III Amfleet cars, some Heritage cars in Phase III, and the original Viewliners in Phase IV. A small window of overlap for that to happen, but it just shows that anything is possible.
Enjoy!
