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IMO, that is a very common repair for the early LP jr, and does not detract from the value of the guitar if it plays/sounds/intonates great. That guitar looks exactly like my old Tobacco '55 junior. The neck was incredible and the P90 was a monster.
The '55 Tobacco Burst LP Jr I bought in 1989 for $300 is on my list of guitars I regret selling (for $5k in 2007). This guitar solidified my love of the P90.
Blew up the picture and adjusted the tone and lighting. Circle on the right looks like a 95. Circle on the left...well only because you said it's a '54 maybe my mind sees a 4.
It does seem a little "new-ish" looking. Maybe it's me but when you blow up the picture of the back of the headstock, I see a faint "9" and possibly a "5". Just curious, what year R9 are you thinking about trading for this Jr?
(Guitar tech hands him the Junior with an alternate tuning...out of tune)
There's a reason Pete Townshend put those big numbers on the front of his guitar.
My conspiracy theory and pure speculation: Someone stole this guitar in the late 70's...and stripped it of all the parts to use on another Junior.
It's hard to tell if there is any original parts on the guitar (the studs look oxidized like they could be original), but the bushings and posts...
Looks like Frank Zappa's work.
In all seriousness, 1958 would be my best guess. Try different lighting and a pro camera on the back of the headstock to see if there are any faint hints to the serial number. It's amazing what a good camera can catch that the human eye cannot (unless of course...