I have only done a couple Ford rail kits, so I don't really have a design that I'm happy with.  The design of the timing cover doesn't really lend itself to a front plate the way Chevy and Mopar do.  Short of switching to an aftermarket timing cover or belt drive, I have found that there are two different ways to attach the front plate.  1.) Attaching to the water pump location.  2.)  Attaching to the lower four timing cover bolts.

Attaching to the water pump location permits a design that spans over the damper and facilitates removal of the plate without removing the damper.

Attaching to the lower four timing cover bolts seems to be the more popular option and is visually more appealing (to me).  The negatives are 1.) Removal of the damper is necessary to remove the plate.  2.) The plate and timing cover are sandwiched together with three or four different length standoffs located between the plate and cast timing cover.  This bothers me on so many levels.  3.) As you are discovering, the plate is very tight around the balancer, alternator, and block-mounted mechanical fuel pump.

I will be so bold as to say, modifying your front plate and/or standoffs is the correct fix.  Compromising your damper or rebalancing your engine to compensate for a poorly designed front plate is not worth it.

Would it be possible for you to mock up your front plate and post pictures of the interference with the damper/counterweight and the alternator.  I can give you a direction when I see exactly what the problem is.

Don't stress too much over the alternator.  Chances are, you can simply trim the plate or drill a new hole in the plate.