Does your system stick up above the engine as high as the alternator?

===> Yep.  See pics.

If it does, I might possibly
cut the manifold on top after the bend, where it is horizontal, have an
extension made and then weld the end back on that the throttlebody attaches
to.

===>  You sort of lost me with this description, but you'll see that there
isn't much horizontal section to work with.  I can't figure out why the
intake is made at an angle, unless it was an attempt to clear the bottom of
the hood on an RX-7.  I've assumed that these manifolds weren't made for
airplanes initially.  It certainly does cause cowl problems in airplanes.  

The reason for these possible changes are because I am now considering
the addition of a turbo

===> The evil seed is planted (maniacal laughter in the background) :-)  I'm
using a stock series 5 turbo, from an 89-91 RX-7.  

Rusty