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Ok maybe an overstatement, but coming from a very tight and sharp EVO VIII, the cowl shake and loose shifting feel of the box may seem worse to me than it is.
I cant help but to notice and focus on it when Im driving over anything other than a smooth road.
Is there anyway to “tighten” it up a bit in those areas? Will a strut brace and a short throw shifter get me a lil closer to what I'm looking for?
Thanks 
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i'm suprised you notice cowl shake. that's not something i'd describe as prominent on the boxster (at least not for a convertible).
as for 'tightening' the feel of the suspension, i installed the M030 sway bars and they made a HUGE difference. you have an 'S', but i would recommend installing the base M030 rear (it's thicker than the 'S' M030 rear). install the 'S' M030 front sway.
Front: 996.343.701.23 (It's $105 from Sunset Imports)
Rear: 986.333.701.20 (It's $ 70 from Sunset)
don't forget the bushings. a front strut brace MAY help with vibration up front, but it won't reduce chassis flex; there are already braces that tie the strut towers to the firewall. from a performance standpoint an additional brace isunnecessary.
i agree with your assessment of the shifter. the stock throw is long and sloppy. i installed a schnell short shift kit, which i like a lot. the shifter had a LOT of side-to side play in it upon arrival, so disassembled and shimmed the lever to reduce play prior to installation. it's MUCH better than stock now. i still see room for improvement and plan on installing an AP linkage when i get a chance (see pic below). hope this helps.