The "thin font" upgrade was an advertised PC Enterprises modification; it replaced the stock font with the thin variant (which is present on all CGA cards, you just need to bridge two points; more info here:
http://nerdlypleasures.blogspot.com/201 ... fonts.html).
In my opinion, there is little reason to do this on a PCjr unless you're hooking it up to an extremely high quality, fine dot pitch monitor (better than the 5153). It also has some ramifications running software that tried to paint graphics in tweaked/hacked text modes, as the "pixels" no longer line up. However, a PCjr board with this modification is very uncommon, so to preserve the value of the board, I would not undo it.
As for the rest of the modifications, your question is answered on the last page of
https://www.brutman.com/PCjr/docs/PC_En ... ations.pdf which states that modification "97514" was "expands memory on PCjrs from 640K to 736K". That's a good mod, since it "recovers" the first 128K of the system lost to video memory, giving you a workable 640K again.