Electrical/Battery Drain Issue

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Driving a 2001 4.4. Replaced the battery a couple of months ago.

Just replaced the alternator and power steering pump. Since getting the new alternator, the battery doesn't seem to charge on short trips. Took it in to the shop and they claim it's getting enough power and I shouldn't expect it charge on such short trips. Wasn't a problem until the new Bosch alternator.

Now to add insult, when it starts, the auto transmission will shift from park to reverse or drive, but is stuck in third gear in drive. Maybe a result of the electrical problems?

Any ideas? Seems like its got to be the alternator or maybe a problem in the starter?