I'm doing the same thing, except I always cut off 2" of the stock header to JB Weld into the can. How much you cut off doesn't really matter since the header usually gets restored to the original length after they are joined with the silicone coupler.
On nearly all of my MCPs the header stub only goes into the can about 1/8". This dimension doesn't seem to be critical at all.
On a 25 size engine a 1.5" x 5.5" can works pretty good. The larger 1.75" can won't let a 25 get on the pipe.
On a 36 to 46 size engine a 1.75 x 6.5" works good. A 2" can won't let the engine get on the pipe, and a 1.5" can makes the needle valve setting erratic.
I'm still searching for a good MCP setup for a 60. The closest I got was with a Bud Bottle on a TT Pro 61, but it still had some mid-range throttling problems.
A 2" x 10" can seems to work good on a 90. But the stock header length is too long and causes mid-range throttling problems. It seems that the shorter the header, the better the engine ran and throttled. I've never reached the "too short" point yet. I suspect that a Bud Bottle is the right size for a 90, but I haven't tinkered enough with it to find out for sure.
Another thing I've discovered is that where you place the muffler pressure tap affects the mid-range mixture. Placing the tap in the mounting flange of the header causes the mid-range to go rich compared to placing the tap in the can.
Getting a big power boost is pretty easy with nearly any MCP setup. But getting perfect throttling from a MCP can be very frustrating at times.
When a MCP is tweaked right, it results in a engine with considerably more power, and throttling characteristics that rival an electric motor. And that's what makes it worth the time and effort to tinker with MCPs.