Mine was done the same way when I got mine for the past owner the tube was welded to the underside of the frame rail. Removed the tube and inserted it through the frame like it should have been..
The rear shackles are quite a bit easier. Theres an existing hole in the frame, which you need to enlarge to fit the tube. It's not easy , as theres a reinforcing bracket inside the rail that makes grinding difficult. A die grinder is about your only choice. Since theres already a hole there, a hole saw wont work.
Rick Kreuziger says he welds a small tab of metal over the hole that has a 1/4" hole in it. This provides a pilot for a holesaw and Rick says this is the fastest method he's found to make a nice hole in this area. Once the hole fits the supplied tubes, slip it in and weld it up.
Greg Zeneski chose to add large washers on the outside for additional reinforcement, which isnt a bad idea and also makes for a cleaner job.
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Here is a picture of mine after it was done the correct way...
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