Anyone who is have trouble with their midway gasket on their 2-piece header and/or stock exhaust manifold should try these methods, as they have worked well for me. This is not to say these methods are the only answer or that they will definitely solve your problem, but they worked for me, and they may work for you. It's worth trying, as these methods will only cost you a few bucks.

FYI: The midway gasket is the gasket in between the two pieces of the exhaust manifold/2-piece header.

Background on the Issue:
My midway gasket on my Megan Racing Header blew.
Another Problem I had was that the studs on my midway flange stripped and I lost a couple of the nuts. What I did was I got the studs out, and bought some bolts slightly smaller than the flange's bolt holes, and used them when bolting the header together. I also used lock nuts and lock washers on these bolts, as I had stripped out the threads in the stud holes.
The midway gasket going bad is a very common problem on Megan Racing 2-Piece headers. Besides from this, Megan Racing Headers are reliable. I replaced it with another gasket (one that I cut myself from a sheet of exhaust gasket material). It blew out again. So i replaced it two more times, having the same problem every time. Eventually I went to the following methods.

Procedure:
Preliminary: (make sure to jack up the front of the car and place it on jack stands!)
1. Unbolt the midway flange
2. Unbolt the lower portion of the header/exhaust manifold from the catalytic converter. Remove the lower piece from the car completely.
(You want to do this, because when putting it back on you will bolt it to the upper header portion first so that there will be no stress on the midway flange, thus lengthening the life of the gasket and creating a better seal.)
3. Scrape the old gasket remains from the midway flanges, and sand the surface down so that it is smooth and there is little-to-no gasket remaining.
4. Get your gasket ready. You can buy a gasket that is pre-cut, but the company that makes the midway gaskets (Megan Racing) for my header has been out of gaskets and usually is, so I did something different. I used a sheet of metal exhaust gasket material, and traced the old one onto the sheet with a pen, then cut it out with aviation snips. The sheet is about 2'x1', and was $15 at Auto-Zone.
5. Coat the new gasket in some Copper RTV Sealant. This is high-temp gasket maker, and will help the gasket have a better seal.
6. Bolt the lower portion of the header/exhaust manifold back on (with the gasket in the midway flange, of course).
Make sure that you bolt it to the upper portion of the header/exhaust manifold first and foremost, before you bolt it to the catalytic converter. Doing it in this order will relieve stress from the midway flange/gasket and create a better seal.
7. Let the car sit over night before running it. The Copper RTV Sealant needs to cure over night, or for the amount of time recommended on the container. It should be fine though in a matter of a few hours. The longer you let it sit, the more you can rest assured that it will last.
8. After it's ready to be driven, take it out, and enjoy your non-raspy exhaust tone, and sealed midway flange!



These are the steps I took, and I now have been driving with my new gasket with no exhaust leaks for about 3 months, whereas before my replacement gasket would blow out in just 2-3 days because I originally did not unbolt the downpipe from the cat. I'm almost 100% positive that it is fixed for good now.

(Update: this gasket held up for at least the rest of the time I owned the car (2.5 years).