Since you are tearing the motor down completely, I would clean it. Not saying to pay your shop to vat it but at least take it to a car wash and pressure wash it. Take it back home and blow out all passages with an air compressor until completely dry then lightly oil the cylinder and lifter bores. Spray the cam and main journals and anything else you are concerned about rusting with WD40 or similar.
Make sure you follow the correct cam breakin procedure and use a zinc oil additive.