l have a 94 mustang gt drop top, and currently have a lightning audio 12'' sub in a truck box and a 300 watt jenson amp. l wanna get something that hits harderand cleaner. l have been toying with the idea of getting one high end 10'' sub with a clean amp, and doing it that way. Whats ur ideas on the best setup for my situation.

Anything other than Lightning Audio will be cleaner & anything other than a 300W Jensen amp will be cleaner & hit harder.lol
Your limited on space to fit a sub box through the trunk opening of a Stang. If u want it to hit hard l would go with 2 good 10'' subs & a good amp with sufficient RMS power. Remember to always go by the RMS/Nominal ratings of subs & amps. That 300W Jensen is most likely a Max/Peak rating which is really only about 150W RMS/Nominal.
l recommend 2 Alpine SWR-1022D subs in a ported box & an Alpine MRP-M1000 amp.
http://alpine-usa.com/US-en/products/product.php?model=SWR-1022D
http://alpine-usa.com/US-en/products/product.php?model=MRP-M1000

Yes you need two 10 and a decent amp that will sound very goond in a mustang with a trans line box.

Convertibles are VERY hard to do sub installs in, but going with a high end sub and a reliable high power amp would be your best option. Consider ficaraudio.com, or soundsolutionsaudio.com for subwoofers and sundownaudio.com for the best amplifier out there (In my opinion) l own the SAZ-3000D, and it is .5 ohm stable and puts out 5,200 watts RMS at .5 ohms, 3000 RMS at 1 ohm, and 1600 RMS at 2 ohms. Go with a good slot vent box, NOT PREFABRICATED!