I have a 1993/94 (im not sure which) JS1000 and I love it!
Ive just had a new EDGE Lo Pro installed because it was broken. I bought it with a Lo Pro and Im not sure what it came with in '93.
I love the Transparent Blue colour as opposed to the Burnt TB colour, the black patches never really suited me! Does yours have the 'JS
Custom' inlay on the 21st fret and does it have the Ibanez stamp thing on the back of the headstock (mine doesnt... so I dont know what happened there!)
As far as I am conserned there isnt a massive amount different. The newer versions have the digital replica of Satch's favourite fret-board, which your and my guitars DO NOT have. I dont think that makes a different, although I have not tried a new version.
These guitars still have the volume and tone knobs which pop up giving you a wider range of sound (I believe all JS1000s have that) and are just all in all a lovely guitar! Id have a '93 one sooner than Id have a 2008 one