the 2003-2004 top will fit your car perfectly. BUT you need teh WHOLE thing. the canvass top AND the metal frame stuff.
the aftermarket canvass tops are JUST the fabric....and you will need a professional installer to remove the old top, and then put the new top onto your stock frame/ribbing.
pedro's suggestion is probably the best bang for the buck - but you have to find the top which is not as easy as just ordering a new one off the internet....
if you are patient and look around you may find a used 03-04 top... someone here did it and had great results... many others have used theGAHH top and like it as well.
how bad is the hole in your window? is it an actual "hole" or is it just a crack/slice? my top recently had a pretty good sized crack - about 1.5-2" long... it is very close to the edge of teh plastic, up close to where the plastic is stitched into the canvass top.... what I did was glue it together using silicone adhesive. I bought a cheap package of loctite clear silicone adhesive at Lowes. the stuff is in a big tube and has an applicator you screw on. then undo the top and open it maybe 1/4 - 1/2 way so all the tension is taken off the plastic window. once I did that, the crack had no tension and it pretty much closed itself so that it was just a slice.... if that m akes sense.. then i put the adhesive on the outside and inside and let it sit a few hours in the garage. i let mine cure overnight and the next day closed it up and when i latched it all shut - no tears. hte adhesive has held for over am onth now.
it's not a perfect fix - if you look really clsoe you can see it is repaired, but at a glance it's very hard to see. eventually, i'll upgrade...but for now -it works.
do you daily drive the boxster or is it a "toy" car you drive on weekends. mine is the latter - so it's rarely out and when it is, the top is down...so i'm not super picky on teh rear window being "flawless" as no one really even sees it..it's either in the garage or undera car cover in the driveway...and when it's out/driven, the top is DOWN!
enjoy the new car! a boxster is such a fun car!
did you paint your bumperettes? that is a must! you can DIY or buy them for not too much. makes the rear end look much much nicer. that was one of my first mods.