Ok, I found some info on "another message board" (linked for me by Battery) and I figured I would cut and paste some of the relevant portions and interesting tidbits here:
On the Gen 1 intake...
If you have a 1st Gen, no need to swap the manifolds. Port and polish the one that's on there right now, and you'll be more than fine
Ive ported a few of them now as well.The gains are nice,especially if you have it tuned afterward
Interesting...anyway, on to the next issue.
On hood fitment with the Cobra intake....
It fits under the stock hood. Look at Dennis R's 96 he's still using his stock hood. You have to cut about a foot long and 1 1/2 high section out of it right in the middle to clear the Cobra upper intake and the d/p unit for the egr though. But that's it and it's not hard to do. You don't cut the sealing area for the cowl seal at all just right up to it.
Don't know exactly what is ment by that; do you just cut the insulation on the underside of the hood, or are we talking cuttin into the hood itself?
anyway, here is something on the IMRC's...
The hard part is getting the Cobra IMRCs to work. On the Mark they are vacuum operated. Vacuum holds them closed and when the signal from the computer grounds the circuit then the sol. opens venting off the vacuum and the IMRCs spring open.
On the Cobra they are operated by an electric motor that bolts to the bottom of the intake. When the computer signals the motor it pulls 2 cables opening the IMRCs. When the signal is pulled away springs close the IMRCs.
So what you have to do is build your own circuit with a relay that operates the motor. Power is on all the time on the Mark EEC for the IMRC sol. where it’s just the opposite on the Cobra. So you will need a relay that supplies power to the motor when voltage is removed.
...So a simple polarity swap using a relay for the IMRCs will work?
Yes in simple terms that’s what you are doing with the relay. An easier way would be to just leave the lead from the EEC cut and use a window switch. You will need to get a tach driver also to activate the window switch though, MSD.
...The Mark IMRCs won’t work with the Cobra intake. The vacuum actuators get in the way of the fuel rails and the EGR tube. So you are stuck using the Cobra IMRC or the 97/98 Mark’s since they are cable operated too. Then you also have to use the Cobra IMRC controller motor box that bolts up under the intake and wire it up with the new circuit.
And on the throttle and cruise control cables...
As for throttle cables, I used the factory Cobra cable but it just barely fits due to the wiper motor being in the way. I mean it works fine and all just very tight and I haven’t had any problems with it. Your stock cruise control cable will work. You have to pull off your driver’s side wheel and inner fender and reroute the cable to reach the new throttle position though. The end that fastens to the T/B has to be switched to the proper connector.
So...can any of you experts make sense of all that?
Do you just need to cut the insulation on the hood, or do you have to cut the hood for fitment?
If you use the Cobra (or '97-'98 Mark) IMRC's, do you get a check engine light due to no input on the IMRC sensors, or do the Cobra and Gen 2 IMRC's have a sensor input?
Any ideas on throttle cables that might work?
Which wires do you need to use to create the circuit to actuate the IMRC's?