Moses,
I agree with you and presented that very question to Clifford regarding simply opening the locating holes in the flange, which is large enough to be able to float the manifold somewhat. The manifold is actually restricted/guided by the exhaust manifold. They indicated that the only header that would work with this intake is theirs, which I'm good with (since I have one). I had considered simply cutting the dowels if it was that important. I think I will find out exactly where the intakes align before I do anything else by using and old intake gasket and doing a rub with some acrylic paint.
i previously used a 4.2 intake with an MC2150, but had to be a bit more adventuresome matching the intake to the head. It worked but ended up with leaks, so I had this setup and figured to use it. Clifford didn't have an adapter to an MC2150, they said that that carb wouldn't provide enough flow. They may be right. I also came across a piece of half inch Bakelite phenolic resin with plans to make my own adapter bringing the Clifford manifold and the MC2150 together. While I have this apart, I think I'm going to make the adapter anyway and just to have it. Who knows what will happen.
To answer your questions, I obtained a sub-1000 mile 4.0 from a Chrysler corporate vendor in 1999 and finally, two years ago installed it in my CJ behind a T-176/D300. Pretty simple. At that time I did my rigged MC2150 since I didn't get the factory injection, wiring, the manifold was designed for port injection, so I couldn't use that with a carb. I then started planning for the Howell unit because of the simplicity of GM injection. I have had several Jeep Cherokees and some issues with factory injection. I could have dealt with wiring, but the Howell unit is basically a three wire interruption into the CJ harness. Add in the availability of GM parts, so on and so forth. I live in Colorado and spend a lot of time in the mountains which are basically out my back door, and I wished to keep things as simple as I could. To me, nothing is more irritating than being way out in the mountains and having a breakdown, even if it's simple, but much worse if it's complex. While I never wheel alone, a strap tow of 20-30 miles is not fun.
I do have a Davis Unified distributor installed, but really liked the MSD timing control setup, so I'm considering the switch to the MSD distributor in order to have that option.
I really appreciate your willingness to spend this time with my project. Any time your name comes up, I come to attention.
Thanks,
Paul