would it be best to go underneath the stang to take a look or should i be able to see it just by openign hte hood and leaning over

 

Check your mounts. Then check your plug wires. Then give a better decription.

 

I'm not sure of the details of this particular engine swap (new or old bellhousing, trans mounts moved etc.), but I've done similar swaps, whe the transmission was moved slightly because of the differnce in the bellhousing. I re-used the original driveshaft but the yoke on the driveshaft no longer inserted into the tail section as far as it did with the original setup. The car was fine at slower speeds, but at higher speed the driveshaft felt like it was out of balance and I would get a shaking that I could feel in the drivetrain. I got the correct length driveshaft for my setup and the shaking went away.