Am using the Energy Suspension polyurethane motor (and trans)mounts and they work great. They filter out the high frequency vibrations that would get through the solids to the body and driver. They do plant the engine so instead of the engine rocking at idle (like the stock rubber ones do), the whole car rocks.
Trans? After much of the same deliberation, I went with a Liberty blueprinted T5Z, .62 OD swapped for .80, and a Hurst shifter. The trans shifts crisp, smooth, and quick, and has been absolutely trouble free now for 15,000 miles. Have 5 useable gears. If I put the 393 stroker kit in, I'll likely change the
oil, and bolt the trans back in. If I break it, I'll get a G-Force T5Z. It's about $1,900, uses re-engineered internals and alloys.
Early T5's were only good for 260 fptq. A stout V6 would break it. Tremecs saved the day. Everyone with a T5 started replacing them with Tremecs. Today, it's pretty much Monkey See, Monkey Do.
Borg Warner did not sit on its hands while their Trans's were being scattered over racetracks and backroads of America. They upgraded it from 260fptq to 330fptq. The Tremec 3550 is rated at 350fptq. The T5Z comes in either of 2 gearsets, 3.35 first, or 2.95 first. The Tremec only offers the 3.35 first. Both come from the factory with .62 fifth (OD), and both can be field retrofitted with .80 fifth gears.
All Mustangs come with 2.73 rear gears and need the tall (3.35) first gear. Most Cobras are running 3.55's or 3.73 for rear gears, and the Tremec (or stock T5) 3.35 first is too tall for the rear gears. Even the T5Z's 2.95 is a little on the tall side for a Cobra.
No Mustangs were factory equipped with the 2.95 gearset so must be retrofitted, or purchased new for Cobra use.
Here's what protects the T5 (and Tremec) in a Cobra. First, a Cobra is 1,000 pounds lighter than a Mustang so the trans will be stressed substantially less during accelleration. Second, a Cobra with street tires will spin the tires before damaging the trans. The achilles heel of both trans's are the shifter forks. They bend when pushed past travel limits. Aftermarket shifters protect the shifter forks with positive stops.
MHO: I think the T5Z is an appropriate choice for a hot street 302, 347, 351, 393, or 408 Cobra with street tires. For track use, the Tremec TKO or G-Force T5Z would be better choices as you're likely only using 2nd, 3rd, & 4th anyway. For strip use, an automatic such as modified C4's, and AOD's will make a quicker car.