Long Live The King?

Thanks in advance for any help you can provide with the following technical question:
I own a (mechanically) stock 2002 FLHRI. Although I have not had any major problems with the bike since delivery, I felt something was just "not right" with the way the motor ran. The idle seemed to be a bit more 'uneven' than it should, the motor would occasionally stall when I let the clutch out from stops and it did not sound quite right, either. I replaced the amber plastic reflector on the downtube (next to the front exhaust outlet) three times due to it bubbling and melting. I then began to think my bike was running too hot and/or something else was wrong.
When the odometer hit 5000 miles last summer I decided to change the air filter. With the filter and box off the bike I noticed a small, right-angle metal tube sticking up out of the induction module that sits behing the air filter can. The open end of this little piece of metal pipe was flared, like it should have a hose attached to it. After making half a dozen calls to as many H-D dealers I finally found a service manager who knew what I was describing to him and what part was missing. It was the 'Induction Module CAP PLUG", H-D Part #90383-98, a little rubber cap that caps the end of the right-angled tube that sticks out of the top of the module. The bike then, and still, runs like a tip-top and the way it should have from new.
My technical question is: Did I hurt my motor by not having the cap plug on the induction module for the first 5K miles? Obviously, I now know that the motor was sucking too much air and was running lean, but, HOW lean? Did I possibly burn any of the innards of my motor or do any other major damage to my bike other than melt a few reflectors?
I will appreciate your help with this more than you can imagine cause I would sure like to rest easy and be reassured that my bagger is now 'good-to-go'.
Pete

Lean can be "mean"

Pete, I can understand your concern, after paying a dealership to upgrade the air in & exhaust out, performance cam & re-jet the carburetor it ran great! After a noticeable performance decrease & 3000 mi. I checked the compression & it was way low. I tore the top end down & found cracked valves. I loaded all my parts up & trucked them to a different dealer, well known for performance/racing work & he made it clear the motor was running hot & very lean. A bit more checking reveled the main jet had not been changed! I paid $2500 to the first dealer & spent $1000 fixing their mistake. My suggestion would go to a dealership you trust & have them check it for you. It can't cost much to check & may save you money & nerves in the long run. Be sure to give the mechanic all the info in detail as you did here & he will know what to look for. Hope I'm not scaring you, but I do think it warrants checking.
Steve