And ... experimenting over for now.
Tried doing the proofed BF400 without cheats and here's what I discovered
-Painting the BF400 during the first cutscene causes it to blow up
--It will not allow you to paint it until CJ is sitting on it, thus causing a death
---I tried running from the hospital (county general) to where the BF would be but it was gone
----Although it may not be proofed, I tried painting it when I got to the roadblock, then ran from that hospital (All Saints) to the spot without looking away from the spot, no good
-----This method still deserves further study - UltimateRisingPhoenix, what was your conclusion about using the other mod shop options other than wheels and colors, did they all crash the game or do other odd things happen that we might be able to use to get the proofed bike without cheats?
Next I tried my other questions and here's what I found:
-You may apply the wheels during the first cutscene, just make sure CJ is on the bike
Mod Shop Menu:
-If you apply the paintjob during the first second or two of the 2nd cutscene, regardless of the car you used in the mod shop, after it says Mission Failed, the mod shop menu returns. You may then choose a different color if you want to or you can add the wheels. When you press whatever button you normally would to exit the mod shop, The BF400 you're looking for is there as it should be, with the wheels and the custom color and of course with CJ on the back seat. I think the timing of this is semicritical because the first marker starts the cutscene, the next changes camera angle so that the Packer can be seen dropping from above. So if you paint the car (bike) before the 2nd marker it gives you the mod shop menu.
UltimateRisingPhoenix, your discovery is monumental. Implementing some of my suggestions will make it so much easier to make your choices. I often times could not get the exact color I wanted because adding the wheels, navigating the menu and navigating to the color I wanted to was difficult in the few seconds it gives you. In a nutshell I would suggest the gamer to add their wheels during the first Cutscene and the color they want during the second. Or, if they want, just add the color during the first second of the 2nd cutscene then add the wheels after the mission is failed. No tripping over your own fingers to get the right menus in the few seconds it gives you. Also my suggestion of driving to the donut shop if it seems Smoke cannot kill the last two guys.