I think he will be okay. You got vet attention when he was sick and that's the best thing you could have done. He probably has some MBD from lack of UVB, but that can be halted maybe somewhat corrected, if you make sure your husbandry is the best it can be.
We can help you with that if you answer the following questions:
How old is your dragon?
How long have you had your dragon?
How long is your dragon?
What is the sex of your dragon?
What size enclosure do you have your dragon in?
What type substrate do you have on the bottom of your tank?
Do you use UVB lights?
If so, Is it a coil, compact, fluorescent tube, or Mercury Vapor bulb?
What is the brand name and number of your bulb? Wattage (if MVB)?
How old is your
UVB bulb?
How close can your dragon get to the UVB?
Do you use a separate basking bulb? What kind and what is the wattage?
What are the basking temps?
What is the cool side temp?
Do you take the temps with a stick on thermometer, a digital thermometer with a wire and a probe end or a temp gun?
Where exactly are you taking your basking temps?
Do you use a heat rock or heat pad?
What do you feed your dragon? Please be specific.
How often do you feed and what time do you feed (morning, afternoon, night)?
Do you gutload (feed) your crickets, worms, etc?
Do you use vitamin or calcium supplements? What brand(s)? How many days a week do you use each of them?
Is your dragon having regular bowel movements (poops)?
Do you
bath your dragon? How often?
Do you mist your dragon or offer water other than in the
bath?
Does your dragon share an enclosure with another dragon?
Have you gotten a vet check and fecal done?
Don't worry - dragons who have suffered all manner of neglect can make a comeback, and yours has not been neglected by any means, so he should be fine. His biggest issue right now is getting over the URI and getting his tummy feeling better after all those meds.
Best of Luck!
Susan