Could a known benign virus ,or a geneticall engineered one cause an auto-immune reaction in a specific targeted part of the body , like one's hand or leg?

Autoimmune (AI) reactions are usually caused by your body's immune system recognising 'self' as foreign, so potentially anything (including a virus that might appear 'benign') that can be recognised as 'self' (e.g., the virus has antigenic epitopes that are similar to one or more of your own proteins) or alter your body's proteins so that they are recognised as foreign, can cause an AI reaction. A good number of AI conditions are tissue-specific although I can't think of one restricted to a hand or leg (!) off-hand, but bare in mind that the causes for many AI conditions are not known.