I've been a little out of the loop, but what happened to Josh making the spacers?
I actually can have a lot of design input here. I've had both previous versions, was an early adopter of the original (second or third IIRC), and was actually part of the initial design process for V2 before the machining was handed over to Josh. I would wager I personally have done the most with intake spacers on my car for a second gen LH owner. If you want to see it for yourself it's all here.
LIM 2.0 + Intake Spacer 2.0 + Plenum Modification (Very Picture Heavy)
Even the V2 design doesn't actually match up perfectly. If you really wanted to do this right you need to base measurements off either the LIM, plenum, or ideally both. To get this effect I took a V2 spacer and reground the openings to match the ported LIM I was making, but the shape is pretty close as is to the LIM. The plenum on the other hand has significantly different ports that don't match up, so there is a pretty rough transition in the air pathways. I went the whole 9 yards of grinding/sanding/polishing out the plenum to match the opened up spacer I used.
It all depends on how "all out" you're interested in going. I tend to be a over the top kind of guy.
I never did anything special to deal with the EGR, which my car has. A little bit of bending but mostly just some skill in re installing the plenum and it seals up fine. I've been running this for something like 7 years and never a leak. I've given tips on it to a few before, but for others it's been hit or miss if they've been able to replicate my success. I used the push gaskets up to the top of the tube method, but you have to be careful not to wobble the plenum while re installing. If it leans to one side it will push that gasket back down.
Josh would weld extensions on tubes for people as you mentioned as an option.
As far as grooves for a gasket. It would certainly make installation easier, but I'll voice a few concerns. The grooves to fit the gasket correctly would have to be pretty deep relative to the thickness of these spacers. It would probably cut half way through the material. Also the aluminum spacers are generally machined out of is very soft, and RTV does an excellent job of sealing the surface regardless of scratches that may end up on the spacer. I'm sure a groove method to use another gasket could be made to work, but I would be weary of taking the chance instead of a fairly easy method that is tried and true.
I'll be glad to share any more of my experiences with you about spacers if you have questions.