Thanks for the replies so far.
JaguarOW, my daughter is only a toddler now, so I've got a few years on this. I'm fairly sure she will want to play some day, based on the way she will insist I play "Old McDondald" for her 10 times a day, but a big part of the reason for this project is for Daddy's benefit. It gives me a cheap guitar to practice mods on before I try it with my American Strat. I figure a 24" scale is small enough to make life easier for a child without being too small for me if she decides she doesn't want to play afterall. Like you, I've also heard that very short scales can be hard to keep in tune, but I assumed it was due to crappy tuners on cheap guitars rather than something inherent to the scale.
Harrison, in general I like Strat trems. I've read on the Fender forums that I might have to file 1/8" off the block of a Strat tremolo to make it fit in the thinner Jagmaster body, which is one vote against it. I'll take a Strat trem over the other Fender trem options. I've heard very little good about the trems on Mustangs / Jag-stangs, and on Jazzmasters / Jaguars. People seem to think they are the weakest parts in those designs, athough I'm sure I'll find people who disagree on this forum.
I was concerned about the ability to upgrade the bridge on the Duo-Sonic because it was a top loader. Most of the top loaders I've found on the web were cheap no-names, but I finally found the Schlaller 475 at Warmoth. I think this is compatible, but I'm not sure. Does anyone know?
I'm also more concerned with versatility than with a genuine Fender sound, although I'm hoping the short scale on a Jagmaster would make the inner coils on P-Rails quack nicely. I want to give my daughter as much room as possible to discover what sound is right for her. The versatility of P-Rails, especially the option for P-90 sounds, is a big vote in favor of the Jagmaster. Putting Strat pickups in a Duo-Sonic would also allow a good (but still smaller) range of options, especially if I used splitable Strat-sized humbuckers. I'll have to think some more on what the best compromise is there.
I do prefer the sunburst and tortise shell look of the Jagmaster over the cinnamon pop tart look of the Duo-Sonic, but I can live with that. Ergonomics are more important to me. If I follow this right, the Jagmaster has the larger body of the two, but its shape is better. Is there any consensus on which would be better for a child?