Scratchbuilding an HO EMD FL9 Diesel-Electric/Electric loco from an Atlas HO FP7 is described in issue 3, volume 15 (Sept. 7, 1984) of the New Haven Shoreliner magazine. The FL9 is about 4 feet longer than the FP7, has different trucks (Flexicoil B in the front and a Flexicoil A1A (a C with the middle axle de-motored) in the rear) and has some miscellaneous chassis and body modifcations — differences in porthole and vent locations, different horn, different dynamic brake fan, and different steam generator details (or HEP generator-set details if you are modeling a current (rebuilt) FL9). The bulk of these modifications are covered in the Shoreliner article, but I did some things differently — these diffrences are described in the document referenced below.
fl9notes.zip Zip Archive containing the scratchbuilding notes as a PDF file. Also included are PDF drawings of the third rail pickup assemblies.
Here are some pictures I took of a "typical" AMTRAK FL9 (AMTRAK #486, sitting at the Albany-Rensselaer, NY station). I found these pictures very helpfull in getting some of the details right.
The pictures below are blowups of the two trucks. I found these very usefull in figuring the dimensions, etc. of the third rail gear.
Photos of the completed model (#486):