I finally got around to photographing and uploading shots of the modifications I made to my Ecto-1 set.
Note: The top shot of the car shows the stock design for the various elements, the bottom shot shows the modifications.
One of the first modifications I made was to add some 1x1 white square tiles (3070) to the sides of the car, covering up the four exposed studs which stuck out on the sides. I'm not entirely sure why this was left like that on the model, as the doors aren't configured with a cut-out like that, I can only guess it was meant to suggest curvature, though frankly I feel it looks better all smooth.
A more recent modification I'd made saw the removal of one of the white 1x2 slopes (85984) on the passenger side of the car, which was replaced with a 1x1 slope "cheese wedge" (18862), and next to it a 1x1 tile with C-shaped clip (15712) sat on a standard 1x1 plate, which would hold the ladder in place. I'd gotten a bit annoyed at myself at how frequently I'd knocked it out of position, and this seemed like the obvious answer.
For the roof rack, quite a few bits were replaced to make them more accurate in my eye:
Radome: For the radome, I swapped out the transparent red 1x1 round plate (which should have been solid) with a 1x1 plate with open stud (85861) in dark red (this will be replaced in standard red when this part becomes available in that colour). The 1x1 round plate comprising the top of the dome was swapped out for a white light cover with bar (58176).
Transparent dish: For the directional dish, I replaced the medium stone grey bar with clip (15519) that held the dome in place with the same part, but in dark red. Like the 1x1 plate on the radome, this will be upgraded when that part becomes available in the normal bright red colour.
Sniffer: On the Sniffer, the 1x1 tile with clip (2555) was changed from a red piece to a medium stone grey piece, and the reddish brown L3 bar (17715) was swapped for a L4 bar (21462) in standard red.
Yellow Tanks: The 1x1 round yellow plates on the ends of the tanks have been replaced with yellow small lever bases (4592) to give them a domed finish. I was originally going to use some light covers slotted into some black 1x1 plates with open studs, however the light covers don't currently come in solid yellow.
A/C Box: I swapped out the 2x2 tile that came as standard for the A/C box, and replaced it with a 2x2 plate with center stud (23893). After a few combinations and tests of a couple of stacked 1x1 round plates, a 1x1 round plate and a lever base, I eventually settled on a white lamp cover for the fan motor.
Another recent addition was the installation of a couple of metallic silver 1x1 round plates on the tailfin rocket cone light covers, to add a big of extra colour, and to have a bit of representation of the chrome on the fins.
Some revisions I'm hoping to implement in the future:
Replace the 1x1 cheese wedges with 1x2 slopes in transparent blue for the light bars.
Part supply and colour permitting, I plan to use one of the new 1x1 round grip pieces (seen on the Ghost Traps for the reboot Ecto-1 & Ecto-2 LEGO set) to replace the four blue spotlights on the roof of Ecto-1, making them more accurate by making them round. Their installation will probably require a reconfiguration of the lightbar assembly, which can be achieved with the aforementioned replacement transparent blue slopes.