there is a special adapter harness from the old rigging to the newer motors for those clearish colored plugs you are talking about....go to your local dealer and tell the parts guy what you are doing and he should have them in stock...it a very common item...i keep them in my shop all the time....
2001 CONCEPT 27SF 2001 250 EFI Merc (sold)
1994 Hydra-Sports 2000cc 2003 225 OPTI (sold)
2005 Kryptonite 23 Custom 300xs Optimax Merc
1999 Progression 27 Twin 300s
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