Croweater, I did a very similar thing with an Ultra Pure column that I have. I added 1000mm of 50mm copper column extension and, at first, joined it with the same brass fittings that you've used.
Before I extended the column I was pulling around 92-94%. After I extended it I began pulling a consistent 94-95%. While the percentage increase isn't that much more, the separation of heads from main run is much more distinct, especially if I let the column reach equilibrium before I start taking off product -- that is, if I wait at least 30 minutes between when the top thermometer gets up to temp and when I open up the take-off valve (from memory the instructions that come with the Ultra Pure tell you to wait 10 minutes). Once I've taken the heads off I also shut off the take off for another 15 minutes to let the column reach equilibrium again before collecting the main run.
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The benefit of the extension comes when you fill it with packing. By filling your extension with packing you radically increase the amount of times the vapour condenses and re-evapourates ('theoretical plates') before it gets to the top of the column and condenses on your coil condensor and either refluxes back into the column or is taken off as product. So fill your extension. I used stainless steal scrubbers from Woolworths. These ones:
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Don't pack them in too tight.
I've been using the extension for about six months and it works great. I ended up ditching the brass fitting and soft soldering the extension to the original column with a 2" copper coupler. I also insulated the whole column.
As for why your column is producing lower percentages with the extension than without, that's got me stumped. I you didn't pull the packing out of the original column, then there's no reason for your percentages to change given that you hadn't packed the extension. However, if you pulled out your packing and repacked it (which it sounds like you might have when you mention that the packing is 4 inches from the bottom of the original column) then the lower percentages might have something to do with how you've repacked it. Packing too tight is no good.
Like you said, these are pretty good columns as is. But where's the fun in leaving the thing as is? You've gotta pull these things to pieces and try to make improvements. Sometimes they work straight up; sometimes not. Keep at it. There's no reason why you shouldn't have it pulling 95% in no time.
Best,
Stilly.