To the best of my abilities, I can help you with any issues you have.
Both "to the best of my abilities" and "with any issues you have" modify "I can help you," so I'd choose to have both of them adjacent to what you're talking about. The actual order doesn't really matter, though, so the other two aren't technically wrong.
Edit: Personally, though, I'd reword it a bit. "If you have any issues, I can help you to the best of my abilities" or something such. None of the original rearrangements seem to really click for me.
Both "to the best of my abilities" and "with any issues you have" modify "I can help you," so I'd choose to have both of them adjacent to what you're talking about. The actual order doesn't really matter, though, so the other two aren't technically wrong.
Edit: Personally, though, I'd reword it a bit. "If you have any issues, I can help you to the best of my abilities" or something such. None of the original rearrangements seem to really click for me.