Hrmm...there's a lot of misinformation flying around.
*Stroking an engine changes the displacement and your compression. You get displacement from the equation: (bore)x(stroke). You get compression from the equation (volume@BDC)/(volume@TDC). If you increase the volume at BDC but keep the volume at TDC the same, you'll increase compression.
*Stroking an engine isn't "bad". V8's and V6's do it all the time, as do I4's (hello LS!). You just have to sit down beforehand and figure out the equations I just mentioned, and ensure that you're not going to risk detonation by increasing compression too much. If you do, lower CR pistons are your answer. However, stroking isn't suitable for high-revving cars. You increase the speed (think of it as mph for your pistons) of the reciprocating assembly enormously. You'll increase torque, but decrease high rpm potential.
*Overboring an engine isn't the be-all, end-all answer to increasing displacement and horsepower either. When you increase the bore, you don't have to worry about the compression. Obviously BTC and TDC volume increase proportionally. You do run into a problem with losing piston dwell at TDC and BDC though. Roughly this translates into less torque, but the potential to rev higher and get more power there. (The pistons don't travel nearly as far, so you decrease the G load on them and everything they're attached to.)


That all being said, if you are intent on doing anything of this nature, go buy lots of books. Study, study, study. Learn everything you can about the engineering aspect of putting an engine together. Primarily the "why's" and "how's". "Why does this do that?" "How does changing this, effect that?" When you've got a good solid understanding of it all, then sit down and decide what you want, and how you want to go about getting it.

[edit] Nothing but the last paragraph applied to your original questions, sorry. Go down and learn about what I said (the how's and why's of engine designing). There's a ton of great books out there, just don't be scared when most of them talk about chevys, fords, dodges and Indy cars. Your engine isn't much different from theres, both are still subject to all of the same rules. Your oversize valve question deals more with head flow, so your best bet is going to be talking to someone who does headwork. Bigger valves aren't really helpful on honda passenger car engines, because it puts the edge of the valve closer to the wall of the cylinder. This disrupts flow, collapses the cone, etc etc etc... read for yourself. With much bigger pistons, and a head thats been thoroughly massaged, you'll want to rethink bigger vavles, because you may or may not have that problem. So... educate yourself, then talk with the experts. [/edit]