So normal driving is fine, you like the spring rate, etc. But when you hit a (common occurance) harsh bump, the shock zips through its travel, bottoms out on your shortened bump-stop, and slams the hell out of car, right?
I don't know who/if anyone is making duel or even single adjustable sport shocks/struts (KONI, Tokico???) but maybe a stiffer valved (like the TRD) shock to keep the soft stock valves from just flying through thier travel, plus a set of stiffer MCU bumpstops could reduce the bone-jarring shock of running out of travel. This weekend I went out to hill country and got the car airborne, coming down hard enough to cause the windshield wiper lever to drop down to high-speed (BANG! "WTF??? Why are my wiper blades on???" LOL!). Here's a link to some reportedly stiffer MCU bump-stops. Anybody from the SF area ever heard of/can vouch for these guys?
http://www.fatcatmotorsports.com/FCMstops_Yaris.htm
Either way, good luck bro.