It does sound like your cats are plugged. I was having a similar problem on my 2000; it made low- and mid-range power just fine, but over 4000 the power started to drop and it wouldn't even rev over 5200 rpm! I took it to Ford and the test they ran indicated excessive backpressure in the exhaust.
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Strike down the unroadworthy!
2000 GT Atl. Blue: '03 Cobra motor - 465rwhp/473rwtq, T-56 6-speed, full MM TA/PH & tubular K-member suspension, Saleen body, 17" Torq-Thrust II's, M/T ET Street radials, and lots more
'94 Rio Red Cobra: All the bolt-ons, 3.73s
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