Joe: I currently have an '06 GT convert which is vastly superior to previous I have owned in the areas you list:
1) Build quality: perfect.....everything fits precisely, no squeaks or rattles. My only complaint: the car magazines praised the solidity of the new (for '05) convert body saying there was no flex or shake. Bull. I later added the FoMoCo front shock tower brace available from dealer which greatly reduced cowl shake.....maybe it is standard now.
2) Leaks: none, as tight as a sedan.
3) care/maintenance: depends on how often you put the top up and down......never put down when wet and I never lower when cold and stiff. I also damp wipe it when dusty.
4) noise: Mustangs have a multi-layer top with liner and insulation in-between. virtually as quiet as a sedan. Ford radios can be set to increase volume as speed increases: not necessary with top up.
5) costs: my friendly dealer wanted $3600 for a "factory" replacement top on my old one.....I went to a trim shop and they did it for $1000 installed - and it turns out they do the work for the dealer too.
consideration: tops were available in Tan or Black when I got mine......I lusted after Vista Blue with tan interior which meant they would not let me order black top......the tan top (like white tops) shows dirt and wear more than black...so I'd recommend you go for the black top in an available combination.
don't order the optional "boot"....that used to be a well-fitting vinyl piece that snapped down over the lowered top.....I paid something like $200 for the "factory" boot when I ordered the car: what I got is an ill-fitting piece of cloth that you strap down over the lowered top and it then tries to blow away. AND, although Ford required me to have a tan top with my tan interior on a blue car, the boot is black !!!!!!!
also, forget ever using the back seat for anything: I have to put the top down just to get back there to clean the side windows.....not meant for human occupation.