Like you mentioned... Check for intake manifold seal leaks. They are cheap (even from HD) and should be in stock. Some recommend the blue James seals with the "lips" on the bottom. I find those difficult to fit onto an XB motor if you dont rotate it or remove it from the frame. But if you insist on using them, pick up a set of stock seals also. I dont know about the independent shops, but most HD dealers will should take them back and refund your money if you dont use them. It would suck to be knee deep into the project to find out the blue seals arent going to work for you. Again, not saying the blue seals are bad, but they can be a pain to fit with the motor in place.
When you rev it up a little, and then close the throttle, you are creating high vacuum in the manifold. If a seal is getting flaky, it can cause air to leak air into the manifold.
IMO, if it sat for 6 or 7 years, you should be looking for problems. Find them while you are sitting in your garage, at your convenience... as opposed to sitting on the side of the road when you need to be somewhere else.