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You might also check out the wiring, from the alternator to the starter, and from the starter to the battery. The battery cable harness can fail/short due to internal corrosion, and the other cable could fail too. Poor grounds to body, chassis and engine can also cause perplexing electrical problems.
My 1996 965 had a bad battery, bad alternator, and bad battery cable harness when I bought it. It took a while to realize all three were faulty as symptoms are similar with all. Now it charges perfectly, holds the charge, and starts easily in 15 degree weather.
Clear the trouble codes from your car and drive it several miles. Hopefully it is just a matter of the computer realizing that all is well now with the new battery and alternator.
Best wishes,
John
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