I installed mine this past July. I've copied what I wrote and how I got around the problems like your having...
Last week I installed the new shorty header from OGTS. I've decided to share my experience incase others will be trying to install this new header. First of all I would like to say that I chose this header because it retained the original exhaust and I could finally get my exhaust away from the intake. First I had to get the old setup apart. By the way, I did this installation with my car on jack stands in my own little garage. Of course, you have to remove the carb and plug the gas line hose. In my case I had to plug the two hoses to my water-choke as well.
I knew I would need torches to heat the 6 bolts holding the exhaust pipe to the manifold so I borrowed my brother in law's set from the farm. It turned out that the torch head was way too big for the job so I headed to town and borrowed my brother's. At any rate, I used a swivel head socket on the hot nuts to remove them, but I still broke two. After that getting the intake and the exhaust out was a piece of cake. The next step would be to separate the two.
I checked out this site and read about some of the horror stories in doing so. I decided to spray the four bolts and let them sit overnight. The next morning I took the whole affair down to my brother's garage, he's a mechanic! His boss lets me use their tools and I decided that an air gun would speed up the process that took someone on this site a day to accomplish. Besides the garage had the special socket and I added a 1/2'' adapter and let her rip with the air gun. The two that go right through the manifold came out no problem. One of the other two snapped, but came out. I destroyed the head on the fourth one.
What to do next? I drilled the head off it, but the two pieces remained locked together. So I put the affair in a big vice and used a hacksaw to cut through the gasket until I got to the offending bolt. Then I used an air hacksaw to cut through it and voila, the two pieces were finally separated and it only took a little less than an hour. After that, I figured that the rest of the job would be piece of cake. Well, the sixth bolt next to the motor mount (by the way I bought all new bolts for the reinstallation) just wouldn't start because there was no way that i could line it up with my fingers or a socket ... NO ROOM!
After some thought, I undid the motor mount, put a large block on my floor jack and lifted the engine enough to remove the motor mount ... problem solved! If I was to do it again, I would put a 2x4 across the engine bay and use ratchet straps to hold the engine at the motor mounts, before removing the entire cross-member. I had done that before when I replaced pistons while the engine was still in the car. Then there would have been all kinds of room to work. At any rate the rest of the job was simply reattaching everything. Also, I don't know which Weber carb everyone else has, but one carb stud is really hidden and it took me a lot of tries to get that nut started. Was it all worth it? ... YOU BET!!
Now it sounds great and hopefully my car will run better on hot summer days. Plus I get all that extra 2 horsepower!! I also find that the car starts better after it has been running and then is stopped for a bit. Before, there didn't seem to be any gas to start the car after it had been parked for about 10 minutes. Though, if you left it for an hour or two, it would start right up. There must have been some air in the line due to the heat-soak. Is this setup a good investment? I think so ... I would do it again in a heartbeat.