Attached Link: Modeling a Smooth T-Joint Connection in Blender

I think you guys are going about this the hard way. I think the tool you may want is the "shear" tool [**ctrl+s** in 2.49 | **ctrl+shift+alt+s** in 2.5x] Given the information and pictures provided thus far anyway, there is/are situations when the shear tool wouldn't work as well or would require other tools to be used in conjunction with it, but I've seen nothing to suggest this is one of those cases.

Anyway, here's a quick tut I three together, hopefully it kinda gets you headed in the right direction, also attached a link to a video tut from Kernon Dillon's Vimeo page, in which he uses the shear tool.

[Step 1] You've got your cylinder like shape, if its capped the way mine was, you want to select the center point first, so you can use the "cursor to selection" function from the snap menu [shift+s] to snap the 3D cursor to that point, altenatively, if you don't have a point in the middle, select the one/two points that would allign with that point, and snap your curso to them instead. Once your cursor is accurately positioned, continue selecting the rest of the points you want to shear.

[Step 2] Make sure your "pivot center" is set to "cursor" the activate the shear tool [ctrl+shift+alt+s]. Move the mouse left/right until it aligns with your background image.

[Step 3] That's all folks. No nasty boolean/knife/cut operations, keeps all quads.

[Click to see larger]

 

One note, give the amount of geometry you have, you'll either have to repeat the shear tool multiple times selecting each row of points, say, one unit for the first loop, two units for the second loop, three units for the third loop, until you get to the amount you need to shear end to match your refrence. The better method to affect multiple rows of points such as you have, would be to use Blender's "proportional editing" / fall-off, unfortunately, I find that horribly awkward to work with.

Hope this helps a little.

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