Looking for some advice...

Have you seen the B&W Operation Sandstone USAF film on You Tube? Also check You Tube for video of Operation Crossroads, an earlier test, as the same aircraft were used in both.  Also use Google Images for Operation Crossroads.  There might have been some color film taken of some of the A-H bomb tests. Also check out volume 3 of Dana Bell's Air Force Colors as it has some color drawings of early A-bomb test aircraft. I would look but can't find my volume 3 at this time.

I'll see if I can get squadron numbers and that sort of thing.

Hm.  I've seen this one before, but I'm looking to build the B-17 that my Granddad controlled the drone 17 from.  As far as I can tell, no color photos of the aircraft exist.  

Here is a photo of one of the Operation Sandstone B-17 drones from Wiki

Units and time frames would be helpful. The Manila/Moresby run I imagine would be after February 1945 after the liberation of Manila.

The B-17 would be natural metal. Theres a picture of one, a drone, on the wiki page about the tests. The aircraft was no longer painted green several years previous.

And...for the new Guinea aircraft, wiki shows a picture of a C-46 flying somewhere, and calls it a C-47 over the Stanley Range, so who knows? Olive drab over neutral gray would be a good guess.

If you had his Squadron numbers, that would be a really big help.

EDIT: there's a possibility he was in either the 22nd or the 374th Troop Carrier Groups. There's a number of pictures of those things online, including Swamp Rat.

They are definitely green machines.

Squadron/Signal publishes a lot of great books on both aircraft. If you go to http://www.squadron.com , I'm sure you'll probably find exactly what you're looking for. Good Luck!