First, seeing that this is your first post - welcome. Hope you find the site helpful
After a few years I am finally getting ready to paint my 69 Mach (428SCJ, 4 spd, Drag Pack, Dearborn car, build date May 12, 1969)
1.Upon disassembly I came across the fact that one of the four nuts holding the rear spoiler on is different. I need to know if the spoiler is factory or an aftermarket replacement so I can TRY to locate one of these nuts
As a little warning - if you show the car with that spoiler you will likely lose points for it unless you claim and have documentation that it was a dealer installed item at the time of original sale.
Even with that claim the spoiler in your pictures is a 70 style or reproduction. Your car appears to have screws attaching (the bracket on the bottom of the spoiler) the brackets to the spoiler when the original 69s used rivets. The nuts are not what was used originally, Ford instead used titanium bolts.
Here is a picture of the original mounting hardware from a 69 Boss
2. Is the inside of the trunk area on a FB painted body color or flat and is there a trim piece that goes on the pinch seam of the wheel well?
Body color - same paint as the exterior and as long as the painter put enough paint on just as glossy
The luggage protector goes on the drivers side wheelwell pinch weld - color of protector seems to generally depend on which plant the car came from
Late fall Dearborn example - ignore the sealer - it was originally painted body color but use and age often takes the body color off the top surfaces of the sprayed sealer
3. Under the car I understand is supposed to be primer (red oxide?) with overspray of body color (Raven Black) the engine bay is eggshelled but how far down the firewall into the trans tunnel does the black go?
"Under the car I understand is supposed to be primer (red oxide?) with overspray of body color"
Well since you listed the car as a Dearborn car - not really. Would instead (given the build date and no original paint remaining on the floor) I would expect to see batch paint being used. Then body color then pinch weld over sprays in that order. Finally a coating of sound deadener on the undercarriage floor pans in certain areas after much of the car was assembled but before driveline and exhaust was installed.
Just one of many threads here - this one includes a few shots of a 69 Shelby I did a few years back - built a couple months before the car your working on. Just to start the discussion
http://www.concoursmustang.com/forum/index.php?topic=10.04.Are the inside wheelwells blacked out or just oversprayed?
Really neither. Rear wheelwells were painted (most if it a pretty nice paint job) when the painter applied color to the fender lip and as he passed the gun (flowing) over the wheel well opening as he painted the quarter panel. He kept the gun flowing so all that paint went in the wheel well onto the back of the wheelwell (over sound deadener) and onto the exposed floor and frame rail there. Including (normally the forward outer edge of the gas tank drop
This picture shows the amount and a small amount of coverage in the rear wheel well. Easy to see that allot of rocks and sand have been thrown up in this wheel well, blasting all the paint off the wheel lip and the paint and sound deadener directly behind the rear wheel
Hope this helps - we can follow any of these questions further if you which. Might check the search feature and past discussions in the 69-70 Shelby and Mustang sections as well as Body and Paint for discussions on batch finished undercarriages