I rebuilt the entire A/C system in a 99 Firebird once, but I immediately drove it to a shop with the A/C belt off and had them vacuum, recharge and test it. I came to the same conclusion as you...that part is best done by people with the equipment and infrastructure to deal with refrigerant. I wasn't worried about contamination because I replaced everything, down to the little seals.

I just paid the 99 once, at the end.

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2001 E53 3.0 5pd