That's a lot of questions. I own the same car, and happen to own the same book you have quoted. IMO, I think some of the information in that book is dated since more advanced suspension components have become available after the book's publishing.
These are my suggestions on some of the ideas in the book:
Engine set back -
This is a serious mod, usually performed for an all-out road race effort. I can't think of anyone here who has done this. If you want better weight distribution, I'd start by using aluminum heads (cuts 50 lbs. off the nose) and relocate the battery to the hatch area. Also consider a tubular k-member and a coil-over conversion with tubular arms -- not only will this reduce front end weight, but also the coil overs and tubular control arms will reduce unsprung weight.
Rear suspension -
Steeda makes excellent suspension components, but if you are going to spend the money (and it sounds like money is not an issue) I would look seriously at converting to the Cobra Mustang's IRS (independent rear suspension). Specific years to look for are Cobras from '99, '01, and '03. With IRS you can use a rear-exit exhaust and won't have to worry about CO poisoning.
Structure -
I would install both the cage and the subframes. The subframes tie everything together and can help prevent the floor pan from separating in the seat area.
Again, just my suggestions based on a little reading, research, and personal experience. Hope this helps!
Russ