not a good TT player but i do play with jpen, so i guess i'll try to help
1) you could take a read of this link to get some insight for yourself regarding sound
http://mytabletennis.net/forum/itc-ryu-seung-min-jpen_topic82621.html
if you value appearances, the rule of thumb is that the grains (lines) of the wood should be straight. the distance between one line and another should be narrow and uniform as well. it is better if you have an "eye" (the ellipse pattern you see on the sides of the blade) on one side or two.
blades made of younger wood look paler and more white compared to older wood.
2) depends on your preferences. chinese rubbers are definitely playable with 1 ply jpen as well, but eurojap rubbers are the ones recommended by most jpen players because you get power more easily out of them compared to chinese rubbers. i switch between euro and chinese rubbers from time to time.
i recommend yinhe mercury 2 with medium hardness if you wanna play with chinese rubbers. plays even better if boosted. for eurojap, there's a lot of good choices. i can vouch for fastarc g-1 and stiga mantra M.
no words on hybrid rubbers as ive not used them yet, but having briefly tried out dignics 09c, first impression is pretty good.
3) use this vid as guideline
https://www.youtube.com/watch?v=fpa9jsoiYIA
don't really recommend shaving it deep like the ones u c on the internet. shave till comfortable but not too much or else your grip would be too loose. the cork piece on the back of the handle is optional, you dont have to cut it off. but it does make transitioning from forehand to TPB smoother if not faster imo.
4) you can use both, but i prefer water-base glue cuz i dont want VOC glue to change the properties of my rubber. though, if you wanna use VOC glue there's no problems at all. my friend uses VOC glue all the time and so far so good.
water-base glue wont damage your blade unless you take your rubber on and off everyday, but u should be careful tho cuz WB glue can splinter ur blade if the glue is too strong. i recommend lidu WB glue (the small one), but i heard nittaku finezip is good. if you wanna protect your blade from splintering, you can look into sealing it with 1 very thin layer of polyurethene or your standard TT lacquer.