[Kurt R Kish]

The 2 guitars are not the same, but they're very similar.
Gtr 1- Squier VM H/H Jaguar
Gtr 2- Squier Jagmaster (H/H)

Similarities:
  Jag body style
  H/H (I tried  DMZ Bluesbucker in both neck positions)
  24" scale
  same neck (virtually)
  same nut

Differences:
  VM Jag- Basswood body
  Jagmaster- Alder body
  VM Jag- top load set bridge
  Jagmaster- Strat style vintage trem (bridge flush with body- springs all tightened)

Sound difference:
I recorded both guitars with a DM Bluesbucker (neck) DMZ Paf Pro (bridge)

Krazyness ! !
The Basswood body top load bridge Jag sounds waay clearer than the Alder vintage trem Jagmaster.

The Bluesbucker is muddier and has less clear high end on the Jagmaster.
This is crazy.  I'm not one to think the body wood has much effect on an electric guitar.
But the Bridge, neck style, scale length and pick ups account for most of an electric guitar's tone.

So I'm considering putting a top loader set bridge on my Jagmaster

[tonejam]

Whether it makes "much" difference is a matter of opinion, but body wood certainly makes "a" difference.
However, it would seem the biggest difference you're hearing is coming from the bridge.

[Matt_B]

What about the pots? What values are they and I'm not just talking about what are they marked but what is their measured resistance?