Smoking depresses your immune system and so will make it much more difficult for your body to clear the infection. This will make any treatments less effective and yes, it will cause the warts to linger because your body won't be strong enough to fight the virus - it is very tenacious. I was just looking up candida injections and the evidence is mixed. There have been some studies that show it is quite effective for some though. Your best bet to maximize the effectiveness of any treatment will be to support your immune system naturally. You'll feel better overall and your body will be better able to deal with any infection. Candida injections cause a localized inflammatory response that may cause your body to recognize and fight off the HPV infection. Keeping your immune system strong involves getting enough sleep, eating lots of vegetables, cutting back on sugar, managing stress etc. Quitting smoking would help immensely as well (I'm sure you know). Smoking definitely sabotages any efforts at healing your body.
Firstly it is rare to have the warts last for 5 years, it has happened but is very rare.
Smoking is a very bad thing for the immune system and therefore, for the genital warts. I read somewhere that a doctor said that out of all the people who did not clear their warts in a good amount of time, all of them were chain smokers. Food for Thought