First off I'll just say, buy dc sports headers or something of premium quality because ive wasted too many Sundays wrestling with these ebay "jdm mugen style type r racing go fast super turbo honda si" headers.
In the past I've tried copper rtv. Copper coat. Exhaust putty. Different gaskets. Made my own gaskets. Used high quality hardened bolts instead of studs. Nothing held for more than a day or two Even though I rechecked torque after the first drive.
There several problems with the design of the middle flange. Its a large physical area with only 3 bolts. The bolts and gasket it comes with are junk. The faces of the flanges are almost certainly not flat. There is not enough material around the exhaust pipe. The flange takes a flat fiber gasket instead of being machined to take a crush gasket or donut.
So instead of welding the flanges together i welded "bushings" into the down pipe. Basically I took a 1.75" exhaust coupler and cut it down the middle length wise and removed enough material to make it fit inside the pipe snugly. I welded the slit back together and ground the welds off. A cutting wheel on an angle grinder or dremel works well to get a nice right angle around the bushings. I crowned the top of the bushings with a flap wheel to give them a nice taper to go into the the top flange.
I cut a replacement gasket out of a 1x3' sheet of felpro felramic gasket material. I am a strong advocate of permatex or loctite copper rtv. Goop the thing up, line everything up, get all your threads started. A good love tap with a hammer and you can start torquing those badboys down.
I did this without unbolting the manifold from the head. Since it took 2 tries to get that to seal correctly. Coppercoat ftw.
So yes the 1/8" bushing effects flow rates etc etc etc... its worth it to me to not be breathing carbon monoxide this winter with the windows up.