Hello. First, I notice you are using the abbreviations ATX & MTX. If you are refering to transaxles with those abrvs, then allow me to inform you that these & regular Thunderbirds are RWD platforms, whereas the taurus is FWD of course. If this is not the case, then disregard this. Next, the 1989 through 1993 model Supercoupes all produce 210bhp & 315 ft lbs tq, and are almost identical in speed. The 94&95 had some supercharger upgrades and other mods, so they produce 230hp and 345 ft lbs tq, approximately. These are slightly faster. Some SC's were exceptionally fast, and ran quarter mile times as much as 1/2 second faster, but these are uncommon, factory freaks, if you will. Now, as for auto vs manual, the manuals are a bit faster, especially when accounting for speed/power shifting. However, the Autos are extremely close, very good in these cars. The 1989-1993 used a regular automatic overdrive, in '94 they switched to AODE, or electronic automatic overdrive. The reason being earlier AODs would sometimes have problems shifting into OD as mileage accumulated. The manual was a M5R2 for all years, (Mazda 5spd Rearwheel trac-lok). In '94 its gear ratio was changed to be more aggresive. Lastly, aftermarket for these cars is not necessarily a plentiful one, but well tailored. There are a few specific groups which make upgraded & oem parts available, at reasonable prices. Being Supercharged, many performance mods such as intake and exhuast upgrades benefit these cars much more than they would other cars. There is a greater amount of airflow to work with, and everything depends on it. This also applies to temperature.. the supercharged airstream causes greater heat buildup than n/a setups, and thus heat reduction improvements have greater affect. Ex: a full exhuast upgrade on an n\a car migh get you about 15 hp, whereas on these cars it can get you as much as 40, in combo with other mods. Theoretically it can be cheaper to mod because it requires less parts to gain the same power than on an n/a engine.. although there is a limitation. Ford designed this car exactly to handle what they put in it, and after enough moding, it becomes necessary to supplement the original design in various areas to support the new mods. Those with more experience could tell you approximatley at what level this would occur.
Is this information satisfactory for your original question? A little more than needed, perhaps, but you can never know too much.