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It sounds like you're using a starting battery. You need a deep cycle if you are gonna do any worthwhile time with the alternator off. If you don't, you'll end up with a dead starting battery very quickly.
Cycling the alternator on the highway will likely not give you much if any mpg improvement. You're simply avoiding the load hit now to take it a few minutes later.
I agree with busypaws about how to do the alternator disconnect. The field control wire is much easier to use. However, I disagree with the idea that its full on all the time now. If there is nowhere for the electricity to go (since its physically disconnected from the battery), the alternator can't put a load on the engine.
One more thing, the mpguino depends on an accurate calibration of injector pulse timing. Altering your system voltage will cause the injectors to open slower or faster, so it is going to throw off the mpguino readings somewhat. Its no problem for the engine to compensate for this, but the mpguino can't. I can't say how much this will effect things, but it will to some extent.
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