Went down to SynroSerge's place for a very enjoyable 4 day work session. Serge came up with what to me is the most elegant and functional solution to my needs. Given that I wanted to move/remove as little as possible but I wanted an I.C. and an ESPAR D5 installed in the engine bay with room for WVO heated filters, etc. and I wanted to keep the battery out of the back seat area, it was a tight squeeze but we did it.
First a comment about the most expensive part of the I.C.

More expensive than all else combined including shop supplies.
By The Way one of the
Beautiful 90 degree 2.5" silicon hoses is for sale.Sawing into the area at the bottom of the Cold Air Intake Flue:

The completed hole:

Note that the vertical fin of metal in the left side of the picture ended up going as well.
The I.C. sat in the space about like this:

Plumbed in the I.C. (Off of a Jetta TDI - Thanks TuneDub)

Going from the I.C. to the Intake:

Underneath it does clear the Catalytic Converter:



We had to take out the Turbo WasteGate Cooling fan. It wasn't working anyway and apparently some are of the opinion that it isn't really needed anyways (wasn't available on most applications). I'm hoping to ge it fixed and moved to the right side of teh engine bay with air supply from the right side cold air inlet flue.
We managed to put the stock air canister back in its place but getting its snorkel to fit in past the I.C. was tight:

There still needs to be some flashing put in place to help guide the airflow so that it goes through the I.C. from the cold air intake flue and not the engine bay and also passes through the I.C. and out the bottom.
Serge is trying to advise against my overengineering tendencies but nonetheless I'm going to figure out some way of getting the $20 motorcycle fan I got from TJ's Cycle (that was a cool looking atmosphere sort of place) to go on top of the I.C. Not much space though:

Decided to stick the ESPAR D5 under the Battery location. It is within the orientation parameters of the installation guide although they probably thought the support bracket would be under the D5. Serge welded some angle brackets to the bottom of the battery shelf with the bolts for the ESPAR support bracket to attach to:

The D5 is then attached to the support bracket:

The D5 is held to the support bracket by hook shapes in the bracket and through body screw. I'm going to use strappping to help hold it in place until I come up with a better solution.
I would've preferrred to have the I.C. laying flat-normal to the air flux but it wouldn't fit with the 1 I.C. hose connection that was at an angle. Perhaps you could take the 1 straight side off of 2 separate I.C.'s and make 1 I.C. that has 2 straight connections but as well I think there would have been issues getting the Air Canister to fit with 2 hoses coming out of the I.C. instead of just the 1 I have.
Cheers for comments,
Cody