My method is a little less polished than his, but I think if done well, it will look just as factory in the end.
First you have to get a booster out of a junk MX-6. It's not super fun. The driver's side foot well in that car is way more confined than ours and there's more stuff on the firewall under their dash. It was a bit of a pisser to get it out but really it's just a spring clip which pops right off, a small pin which comes right out and four nuts. The spring clip is really hard to reach, and one of the nuts is blind and nearly impossible to reach.
Anyhow once you get it off, it looks like this...

That lip protrudes down into the booster about 20mm. The 6's stock master cylinder has an o-ring that seals inside that bore. The problem is that our GS master cylinder is slightly larger in diameter than this opening. Projectzemx3 chose to grind on the OD of the master cylinder housing to get it in there. I chose to remove that inner lip altogether and make the opening large enough to fit the master cylinder in.
Using a dremel cut off wheel I slowly cut into the lip all the way around until it came off and fell into the booster...


I was easily able to pull the cut piece out afterwards. I then used a drum sanding bit to smooth the edge and enlarge it all the way around. You don't have to take off very much and it only took a minute or two of sanding to make it large enough for the master to slide in. So that's step one.
The next big problem is that the GS master and the 6's master have different configurations. Note the obvious differences...
MX-6 Master Cylinder...

MX-3 Master Cylinder...

It's hard to understand without holding them in your hand, but on the 6, the sticky outy part is just a shaft for the internal seal to seal upon when the piston is depressed. The pushrod of the booster slides all the way in down the middle of that shaft. On the GS the sticky outy part does act as a sealing surface when the brakes are applied, but its stock pushrod only slides in about 17mm deep. It's actually hollow on the other side and that hollow cavity acts as the primary piston. It's a bit complex to understand unless you're holding it in your hand as I said...but the point is that the 6's pushrod is about 25mm too long and won't allow the GS master to bolt up nicely. You have to shorten that pushrod.
I used a cut off wheel again and got down inside there and cut it off. I made sure to undercut it a little. You can always grind a little more off but if you cut it too short, you're screwed.

I guess one downside of this method is that the pushrod is no longer adjustable. My thinking is, I will adjust the length of the pushrod so that it just places a very slight pressure on the master cylinder's piston when I bolt it on. I think that will work just fine.
The last thing is how to seal it. You'll notice on the stock GS booster there is a seal in the booster that seals against the pushrod so the master doesn't have to seal anything. But we removed the 6's sealing surface in step one. I did some measuring and the base of the GS master is almost exactly the right size for a metric o-ring M4 x 50mm. Possibly M3 x 50mm...I'll be checking with both to make sure I get a good seal.


I'm not quite done. I have to fine tune the length of the push rod. I have to sand blast the booster and repaint it. I also have to spend a little time shining up the face where the o-ring will sit to promote good sealing. Also as Projectzemx3 pointed out in his post, you have to grind a bit of the lip off of the fire wall as the MX-6 booster is larger in overall diameter than the GS booster. It's really important that you clean the booster out really well when you're done. Your intake manifold will suck all the filings and dust and crap out of there like a vacuum cleaner when you start the engine.
Having done all that, the straight neck KLZE IM should have clearance now. I have read something about how he still had a bit of an issue with the reservoir hitting the linkage. I'll deal with that when I get there.
Hope this helps some of you.