I installed a MGW in my 2006 Coupe via the lowering transmission method. Correct me if I'm missing any steps, but don't bash my posting if you disagree - this is just how I remember doing it.
Inside the car I removed the driver seat to gain better access. I removed the center console including the center glove box and all the plastic around the shift lever. There is a jam nut holding the shift knob in place...it's tight. Be patient and it will come apart. Don't sit there and twist the shift knob. That is not how you remove it. Once the jam nut is apart, the shift knob will unscrew. There is a rubber inner shift boot that is riveted in place. You can either destroy the rubber boot (dont do that) or drill / air hammer out the rivets. Taking out the rubber inner shift boot allows you access to remove the old shift mechanism and install the new one from inside the car. Once you remove the inner shift boot you can access two of the four screws holding the shifter in place. Go ahead and remove them. Basically, there is a screw on each "corner" of the shifter.
Underneath the car you will need to remove the belly pan which is a bit of a pain. Once removed you will see the transmission brace. It runs right-to-left underneath the transmission and is held in place with (I believe) two nuts/bolts (one on each side). Support the transmission with a jack and remove the two bolts. Note, this is a great time to replace the tranny mount since you're already under there!!! Lower the jack slowly and the tranny will drop down about 8 inches or so. From this angle under the car (which had better be supported with really strong jack stands) you can easily reach the other screws holding the shifter in place. You might try removing the reverse switch if it's in the way. You will know what it is when you see it....because it's in the way.
Once all four bolts are off, I went back inside the car and pulled the shifter out from the top. It's pretty straight forward putting the new one in, but be sure to line up the "ball and socket" other wise the shift lever wont do anything. This is important!!! You dont want to put everything back together only to find the shifter "ball" is not aligned.
From here just button everything up in the reverse order and enjoy!