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My friend bought the paxton kit from brenspeed on his daily driver and has had it for 18k miles (almost 2 years) and he hasnt had any prob yet. I've also heard good things from the roush s/c
You can run any supercharger you want its just up to what hp you are looking for. I roush supercharger is good for about 435hp like on the roush 427r, but you can also run a whipple on low boost so it wont damage anything. But if you dont plan on going too high in hp stick with the roush, they have a warranty on ford if you put one on your motor.
If I were you I would recommend the roush M90. It's very affordable, I've heard very safe & upgradable to make over 400hp to the wheels if you decided to run more boost in the future. Justin from VMP tuning has a pulley & custom tune for the unit that will get you there if you wanted that extra kick I described above. I'm in-between that system & the Novi 2200 SL.