Hey Charles!!!!
First of all, where are you? You might be able to get some experienced SOC help right from your area to help out.
I don't agree with Patrick, though. It is pretty easy to lower (or raise) your VW suspension, once you get past getting the spring plate off of the bottom stop (BIG pry-bars work well there), and the info I worked up should be more than enough to get you where you want to be. Heck! I used my own info and ended up right where I wanted it to be (but I'll admit that even I was surprised!!)
To get to your questions:
1) what should the appropriate clearance be?
Answer: Whatever looks cool to you. Mine used to be just about right in the front (for my liking) but the back end was up a couple of inches too high which looks good on a street rod, but not on a Speedster, hence my effort to lower it. Speedys seem to look good with the tops of the tires just a little up inside the wheel well (check out a lot of pictures in the photo section) so shoot for that look.
2) should I lower the front end as well, and if so, how much?
Answer: Yes, lower the front end by using adjusters, either Avis style (from Gene Berg) or the bolt-type from CB Performance or Kymko. I used Avis style, lowered so I have an inch or so of tire up inside the wheel well, did NOT opt for the lowered spindles, and have noticed no appreciable handling difference compared to my wife's Honda. If I were to do it again, I would probably use the bolt-style adjusters, since Avis style are harder to adjust. Make sure you do BOTH top and bottom torsion tubes in the front. BTW: the Speedy body is a LOT lighter than the original Beetle Sedan, so the spring rate (stiffness) is more like a sports car. Even with the engine weight back there, it won't move much over bumps and so forth, so you can get by with just a few inches between the top of the tire and the inside of the top of the wheel well. Don't sweat it!
"I want to look cool (or as cool as a 54 year old guy can look), but I don't want to sacrifice too much ride comfort"
Yeah, me too, born in April of 1950 and want a Cadillac ride - it won't be, but it's really not very harsh, either.....again, a lot like Kathy's Honda, only tighter in corners.
3) If I put in lowered spindles (and if so, what size), what would be the best anti-roll bar to use? Will a stock one fit upside down, as I've seen discussed? Is there something better?
Answer: This could get us a lot of discussion, believe me. I've seen Kirk at VS use the stock Beetle Sway Bar mounted upside down on a lowered front end (without lowered spindles) and it seems, to me, to handle just fine. I have a 3/4" "Sway-Away" bar from CB with stock spindles and, while it corners really flat, it might have added a bit of stiffness to the front end - maybe not so bad. I have not noticed any "bump steer" or stiffness of the steering with lowered, stock spindles (one-hand it in and out of parking spaces and such). I'll also be adding a "Sway-Away" rear roll bar this Winter, mostly because it was given to me as a gift. I'll try it out and see what I think, but when I get to installing it I'll be where the roads are mostly straight so assessing cornering performance might be tough. (Guess I'll have to drive over to I-95 and hit an off-ramp really fast and see what happens!)
Also, don't forget that I run 6" rims front with 205X16's and 7" rims back with 225X16's - a LOT of tire for this size car, and those big meats help cornering a LOT...like the rear end has never let go on a fast, hard-cornered clover-leaf.
Hope this helps, and let us know where you live - maybe some of us could come over, bring some micro-brews and help out.
Gordon