14 escape

Replacement motor when I bought  car on way home from cloumbus Ohio spun rod bearing drove straight to shop cylinder 3 rod bearing so needed motor Replacement bought one used with 116000 from reputable savage yard shop puts motor in with everything new timingbelt plugs valve gaskets water pump shop let's run for hour in shop fan kicks on off idles good drives in city does OK but needs some more power only about 80 percent tells me might need to burn cleaner and stuff off but good no codes in pcm try to drive hard to get past 50 miles hour bring back no codes he can't figure out problem bring to new shop says cats are clogged holding 4 pounds of pressure told them to fix it then 1600 for new cat still no power surges now at idle almost like miss but not quite again no codes the 2nd shop thinks timings off a tooth maybe 800 to recheck timing now runs good enough to drive but still not right rough idle and bad gas milage and powers about 85 percent now and goes 80 on freeway but has dead spot at 31/2rpms to about 4 rpms in 5th 6th gear then pulls good again its almost a miss but not quite both shops say all numbers are in correctly in the parameters they are supposed to be but on my scanner it says miss fires last drive cycle  10 times but doesn't say which cylinder or why just  miss fires at certain seconds of motor starting and at what rpm but not enough  to set check engine light or specific cylinder any advice would be great I'm 6000 in and still not running good thanks