Did he also change the blower regulator? I think one generally changes that when they change the motor itself, but maybe he didn't. If that's bad, it would cause flakey blower behavior. Once you get the battery/charging issue sorted out, I'd try replacing the blower regulator and see if that does the trick.

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1987 300D, arctic white/palomino--314,000 miles
1978 240D 4-speed, Euro Delivery, light ivory/bamboo--370,000 miles
2005 Jeep Liberty CRD Limited, light khaki/slate--140,000 miles
2018 Chevy Cruze diesel, 6-speed manual, satin steel metallic/kalahari--19,000 miles
1982 Peugeot 505 diesel, 4-speed manual, blue/blue, 130,000 miles
1995 S320, black/parchment--34,000 miles (Dad's car)