Harrison,
I've used the trick to bypass the 100 option limit as well, and also ran into an issue similar to yours. The solution is as follows:
The field that is linked to the multi select (the one that has more than 100 options), mirror that on a formula field and link the formula field to the multi-select. So make the formula field [Formula Field for Multi Select] = [Original Field for Multi Select].
Before you import, make up a silly rule and put it in your formula field. Comment out your original line and put something like "Fake Text" (so that the only possible option for the multi-select is now, 'fake text').
Now do your import, it should work. Then go back and change your formula field back to normal (the mirror).
In fact, for anyone using this trick it is good to link your multi-select to a formula field. The reason being, if you ever try to change something in your multi-select field (even just try to change the field name), it won't let you save. It will tell you there are too many choices. If you have it linked to a formula field, you quickly go change your formula field to force it to under 100 choices, make your multi-select field changes, then change your formula field back.
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Mike Tamoush
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