Really, I appreciate all the encouragement from everyone and I may go back and mess with this some more but not at this time. I like the o-ring idea, but my biggest concern is still how thin the plenum base is, any machining/welding of it will either make it thinner or warp it really bad or both. Aluminum moves in all directions .0000012" per degree of temperature. More mass is better.
Just a couple of issues to note:
1. When I started the injection manifold (4-5 years ago), no one made a bolt on.
2. I can't weld anything thicker than 1/4" aluminum with a 200 amp tig welder successfully (i.e. 1/2" to 1/4", 3/8" to 1/4" etc.)
3. My bandsaw doesn't have a large enough throat to cut the base of the plenum off to replace or build up areas that need help
4. I don't have a mill
Good things that come of this:
1. Plumbing a single inlet is easier than two
2. I can add a MAF sensor (that I already have) easier
3. No gasket to leak
4. I know the edelbrock manifold will work
5. More options for placement of components/lines/wiring etc.
It's a good thing
For the gasket consider this...?
mill a .032" o-ring channel in the intake all around the outside of the area you need to seal. The inside who cares if it leaks inside the manifold right? Maybe spot face the screw hole you have in the middle for a small o'ring to seal if it's a concern? Then either get the right size o-ring ( .047" think standard) or buy a spool of o'ring cord and crazy glue the ends together ( make sure they are cut reasonably square) put a dab of silicone or gasket sealer on this joint. I for 25 year have built blow molds for plastic bottles and we use this method for water lines that see 90 psi and it doesn't leak!
Your engine might at best pull what 20 psi?Being a captive o'ring it can't go anywhere!
For more clamping pressure for the intake and plenum, I'd use 5/16 fasteners? Get some round aluminum rod say 1/2" ?. Drill in the plenum where you want the bolts to be 4,6,8 places? weld the rod into these holes. then weld the same aluminum rod in the same locations on the intake.Mill everything flat again after welding. Use the flat head socket capscrews you have now to locate it together. Then drill through the 2 bosses( aluminum rods you just welded on the plenum and intake) with the tap drill size. Separate the intake and plenum tap the plenum for the 5/16 ( or what ever size you chose?) and drill out the intake for the clearance size for 5/16 ( or whatever?) Then you can bolt it all together from the bottom of the intake( off the engine)
With the intake port mismatch, did you try it back on the engine your using without the gaskets yet? If it's better than all you have to do is cut the intake till it fits? Slot the mounting holes if you have to? You have a mill and a welder right? No such thing as "won't fit" !
DONT GIVE UP! DON'T LET IT BEAT YOU! 
