A few things you have control over:
Hygiene, wash your hands a lot. You’re getting food poisoning frequently? Change your diet and eating habits. When I’ve suffered that in the past I avoided going out for long periods of time. Also, wash your hands. Drink excess water when you feel the “twinge” of a cold or other illness coming on. I drink twice as much water when I feel like I’m fighting something, with the goal being clear urine, and frequent once an hour bathroom breaks. Did I mention hand washing?
And, the best is just sleep and rest. Strive for an extra hour of sleep if you can when you’re feeling something coming on. I’ve learned that I can move my easy endurance rides to an evening and it won’t affect my sleep too much. I normally prefer all my TR work to be done in the AM but will prioritize sleep and rest when I’m feeling less than fresh or believe I’m fighting something. Getting that extra sleep is more important than the endurance or recovery ride I may have scheduled in times of duress. Think of the big picture in moments like that.
Learn to be super flexible with your plans. I think it’s best to skip or reschedule break through and HI days when you’re feeling run down. For me, either taking another rest day or replacing a HI day for an endurance ride or recovery ride seems to work well. Check in with yourself often and try to get back on it when you’re feeling better. Also, learn to pull the plug on tough days when your HR seems lower or higher than it should for a given effort and your body isn’t responding to the effort like it should.
Lastly, vitamins, homeopathy, and other gimmicks are only good for one thing - removing you from your money. Use your money for medicine that fights the symptoms like decongestants, cough drops and sometimes even cough medicine. Zicam and other products like that are snake oil and should be avoided.
Sleep, extra hydration, hygiene and a reduction in training intensity. Focus on that. And stay healthy. And of course see your Dr if you think any of this is a chronic condition.
To your second question - move on with your annual plan just as soon as you’re ready. You may need the chance of pace after spending a ton of time in the base phase. That could be the change you need to see a significant FTP increase. Your body likely needs some different stimulus at this point. Good luck and stay healthy!