BTW, I know this car has a 1968 hood. I noticed it immediately. I assume some cars were built this way as I have seen a few 1969 Coronets before with 1968 hoods.
Well, I'll throw in my $0.02 on this one as well, since I'm somewhat familiar with '69 Super Bees. I've owned mine for 43 years now.
1st, the hood looks legit. Without the Ramcharger N96 option, the Power Bulge hood was Standard issue.
2nd, as someone already mentioned, the Air Cleaner assembly is NOT a '69. It looks like a '70 style that would be on say a Challenger 383, I'm sure it was used on others as well.
3rd, the interior seat upholstery, front and rear, is NOT factory '69 Super Bee. In fact I don't believe it is '69 Coronet upholstery at all. Not sure what it is from. On second thought, this car has bucket seats (option code C55), so MAYBE with buckets you got this funky upholstery?? Door panels don't match with Super Bee's I've seen either. Steering wheel does not look to be correct for '69 either. Anyone know for sure about any of this?? The rest of the dash looks good and correct for '69. Can't see the tach/clock very well in the photos, does it have a Tachometer with the Clock on the Rallye cluster? The fender tag is coded for both A62 (Rallye Instrument Cluster) and N85 (Tachometer). The A62 supposedly INCLUDES the Tachometer, so therefore the N85 code would seem to be redundant? Just seems odd.
4th, notice the door handles. They have the BLACK plastic buttons which were used on early model year cars. This fits perfectly with the SPD (scheduled production date) of August 15th, 1968 on the fender tag. Also, the tail light lenses appear to be the "early" type as well. Both of these items changed to a different style somewhere around January 1st 1969. So, both of these look legit. However, the tail light FINISH PANEL is not correct for a Super Bee. Either this was changed out from another Coronet model (Coronet 440?) or the original finish was removed and not restored to factory OEM. Same with the finish on the headlight bezels. They appear too "Bright".
5th, On the passenger front fender, it is difficult to see if there is a "Pentastar" on the lower portion of the fender. If there IS one there, it appears to be too far back, too close to the door edge. If it is missing, that is another indication of sheet metal work that has been done, possibly incorrectly. In addition, the one picture that shows the passenger side door jamb area with the door open, just seems a little peculiar to me. I'm looking at the seam where the quarter panel meets up with the door jamb and it just doesn't quite seem like a factory job. Kinda looks like some rough weld bead in a couple places?? I don't know, maybe it is factory???
6th, fender tag is coded for a BLACK tail stripe (V8X) and this car now has a WHITE stripe.
7th, Exhaust tips are PLYMOUTH, not DODGE.
8th, Of course the spare tire hold down bracket is missing from the trunk, but you stated that the trunk floor had been replaced. Just another detail overlooked by the shop that did the work. I call it "shoddy" but you may be OK with it?? Also, as a FYI, there looks to be a trunk light switch installed on this car. Usually this is part of the A01 Light Package option, this is NOT coded on the fender tag. Again, not sure how this happens.
I guess that's enough analysis for this one, hope this helps you with your decision. Overall, probably one of the better cars "for the money" that you've been looking at that I'm aware of. Good luck!
edit: Looks like more info has been posted while I was composing this reply. Others have brought up some of the same issues I've pointed out.