On all Volkswagen VR6 motors they have very shitty ignition coil packs that crack on the outside casing allowing for arcing of sparks causing backfires etc. These problems are also slightly more noticeable on rainy days.
You can solve your ignition problems once and for all by swapping to a Ford ignition coil. These are known to be extremely reliable and Ford usually builds quite stout components.
You can use quite a few different Ford V6 coil packs however the older ones use a hybrid spark plug which has a slightly different end than the stock VR6 spark plug wires. The following list of coil packs are 100% compatible with the stock VR6 wire.
FORD E-150 2001-2003 FORD E-250 2001-2003 FORD ECONOLINE 2003 FORD F-150 2001-2008 FORD FREESTAR 2004-2007 FORD MUSTANG 2001-2004 FORD RANGER 2001-2008 FORD SABLE 2001 FORD TAURUS 2001-2007 FORD WINDSTAR 2001-2003 MAZDA B3000 2001-2008 MAZDA MPV 2001 MERCURY COUGAR 2001-2002 MERCURY MONTEREY 2004-2007 MERCURY SABLE 2001-2005
If you want to purchase one, RockAuto is always the best: https://www.rockauto.com/en/catalog/ford,2003,mustang,3.8l+v6,1415078,ignition,ignition+coil,7060
The mounting holes are almost identical however one side will be a half inch too short so you need to add a small bracket.
Here are some photos of the wiring and setup. You will attach the spark plug wires up the exact same way as the stock unit.
Here’s a decent video that I found:
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