Jeff -
 Not sure why you've concluded to go with a new set of aluminum framed windows, if the problem is leaks with the old ones.  It does seem (at least to me, FWIW)  that the frame and glass system will probably always be more leak prone, just because of the design -- there are just more potential failure points for leaks to develop (I'm assuming that's could be one reason why Catalina changed the design to frameless at a later point). 
    But if you are going to stick with the aluminum frame concept, why not just remove and reinstall the old ones with fresh sealing compound (since you're going to have to seal the new ones anyway)?   Its not as if the old frames and glass themselves have worn out, and, as you indicate, you are getting "essentially the same as what originally came with the boat" ...in which case the real issue is the sealing.
   As you know, (as we've been discussing of late in another thread on this subject  www.catalina36.org/forum/technical-discussion/replacement-windows-87-c36 ),we replaced ours with frameless windows,  but if you hunt around on this site you'll find some older threads where other members discussed in detail the process of re-sealing the frame-style windows that our older boats came with. See, e.g., www.catalina36.org/comment/40844#comment-40844.  Seems to me you'd save yourself the 2 grand cost of the new windows, and would just be looking at the labor costs, which would not be much different either way (other than cleaning the sealant off the old windows).