The GTS is a stripped down version of the GT. It was only made for a year and doesn't feature power windows or a spoiler (there are probably some other minor things that weren't available as well).
As far as which car to go with, it's really a question of what you're looking for. I'd go with the convertible, but that's because I've always wanted one. If you're more interested in performance, go with the GTS. With the mods you've listed you would be in the mid-13 second range. You would need a supercharger or a good set of aftermarket heads to get in the 12s.
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Eric - 89 Mustang LX coupe
302 - Cobra Intake - GT40p heads - TFS stage 1 cam - FRPP 1.6 roller rockers - Naturally Aspirated
3:73 gears - KYB shocks and struts - Eibach springs - HPM Mega-bite Jr lower control arms - HPM upper control arms
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