Unless that piping was like 5", it should have NOTHING to do with the fact you can only reach 55 mph on the freeway. There might be a little something to do with it, but the exhaust isn't at fault.
A cat-back exhaust on a lightly modified Honda Civic has nothing to do with performance and everything to do with noise. Assuming the piping is 2.5", it won't affect your acceleration at all. The size of the resonator, likewise, is as equally unimportant. Its job is to surpress sound. The size may increase or decrease backpressure slightly, but again it's not enough to notice.
Your problem is definitely tranny related. Why you could get to 85 with a Flowmaster and only 55 with a Meanstreak is beyond me, but presuming both were just cat-backs that are simple to install, your "top speed" problem is related to something else.
Is your clutch slipping? Put it in 5th at 30 mph, and floor it. If the RPMs shoot up while the MPH doesn't change, it's slipping. If the car accelerates slowly and bogs a little, it's fine.
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