SP is right. I have 3 540-s, had a 540-r that I heavily modified, and I have a JS6. Completely different feel on all of them. As someone else pointed out, it's easy to pick apart the components, and show that the trem/pikcups/etc are better on the JS1000, but it's just as important that they are made in different factories with different customers in mind.
I recently starting a new project - putting a cheap RG neck onto a JS600 body. It's going to be a unique/cool looking guitar (a budget JS2400). The neck and body are both in great shape, and I've put a Gotoh bridge on it (basically identical to the JS6). But as I play it, it's just obvious that it feels so different due to the neck being off of a korean or indonesian RG. A good setup will help, but it's just never going to play like the JS6 or my Japanese made 540-s do.
If it were me, I'd look for a great deal on a used JS
-100, and then keep saving for the JS
-1000. If you find a great deal, you'll sell it later without losing money on it. You can spend a lot of money on doing these mods yourself - pickups, better Edge trem, etc, and still won't get it all the way to the JS
-1000. Plus, you may find that you get all you need from the JS
-100 in the long run.