While it's still undetermined why certain customers have issues lining up their inner and outer fairings, the FLH models have had the same part # for the outer fairing '96-'13. The inner fairing was modified in 2008. We have sold many painted inner fairings without issue. This problem is manifesting on wrecked bikes which could add to the alignment issues.
1996 - 2007 Inner / Outer Fairing FLHT
58236-96 '96 Outer Fairing
58497-96B '96 Inner Fairing
58236-96 '07 Outer Fairing
58497-96B '07 Inner Fairing
2008 - 2013 Inner / Outer Fairing FLHT
58236-96 '08 Outer Fairing
58497-08A '08 Inner Fairing
58236-96 '13 Outer Fairing
58497-08A '13 Inner Fairing
'96-'07 Inner Fairing
'08-'13 Inner Fairing