The 2nd gear pop out is somewhat of an known problem with some of these boxes, and I doubt it'd being caused by the linkage. The grind you started experiencing was likely just a worn synro.
There is a company in CO called GBox, and they specialize in Porsche gearboxes. They have a permanent fix for this problem, which they typically do whenever they have one apart for a rebuild. They are likely getting my gearbox soon for a freshening, and while it's there, I'm having an LSD installed.
Was the gearbox fully rebuilt when it was apart? Seems like an AWFUL lot of labor to only fix one gear (and at that, it doesn't like your problem has been fixed). I would speak to the shop that did the work, as its very unlikely that your warranty company is going to pay twice for the labor.
Sorry to hear about your ongoing frustration.
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Boxster S
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