Mechanical Issues Exhaust And Transmission

The manifold studs should be servicable by a reputable shop. Anyone that breaks your car worse and leaves you hanging isn't reputable in my book. As you stated, another option is to install shorty headers. For the labor involved, there is very little power gain. If you go through the trouble, get a set of factory manifolds for cheap or do it with long tubes for a nice bump in power.

The T56 from the cobra will bolt up with the correct flywheel, clutch, ect. It seriously isn't worth the cost unless you are planning to make big power in the future (like more than 450rwhp). The advantage of the T56 is strength, and you are no where near to making enough power to scare a stock T45 or TR-3650. One of these 5 speeds would work well for you too. Not sure if you will need to switch the computer, but my past experience has been that you can trick the computer to working with the manual.