It sounds like you had a transient infection, probably bacterial (staph, strep, and the like); nothing else is likely to cause lymphadenopathy that flares up and resolves so quickly. Most likely nothing sexually acquired. It might or might not be related to the penile nodule, which could be an infected/inflamed cyst--but doesn't sound like an STD. However, I can't say much about the itching.
At this point, I suggest leaving the penile bump alone; avoid the temptation to repeatedly feel for its size etc, and definitely no squeezing etc. If it just goes away, don't worry further. If it persists a week or two, or if it any time it obviously enlarges or gets inflamed, see a health care provider. But if in doubt, of course see a provider anyway; my advice is not a substitute for personal health care.
Good luck-- HHH, MD