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I threw a rod in my orignial engine back in March in put in a used 3.1 with 74K. Just recently I've noticed a considerable vibration that seems to be coming from the engine. It's very noticeble when I'm in 3rd (it's an automatic) going about 45 as I get a nice foot massage from the accelator pedal but this quickly gets irritating. I'm OCD about my car and I don't know how much longer I can put up with it. Same thing happens when you get to a stop light with the foot on the brake, if you put a cup of water on the dash it looks like the T-rex from Jurassic park is sprinting towards my car. So where could this be coming from? I really don't want to go and pull the motor again but this vibration can't be a good thing. I'm pretty sure that when the engines were switched that the engine mounts were not replaced - yeah I'm not to happy about that seeing as that should be done when your down there anyway. I think I'll have some words with my mechanic if that turns out to be the case. Other than that, the car gets proper maintenance every 3000, oil change, plugs, filters etc. Any ideas, suggestions would be greatly appreciated. Thanx.

Definately start with the motor mounts.

Pop the hood and have a friend watch the engine as you shift from park to drive to reverse etc.  Too much movement is a pretty good sign that your mounts are toast.

Any clunking when you put it into drive and get on the gas or anything?

Ditto on mounts.  Makes a huge difference.