Genital warts are external growths over the parts involved.In females,it involves Vagina ,cervix
As you are taking treatment,they will be subsided soon.
that is enlarged in your case may be due to Bacterial infection.Please take a Good antibiotic with combination of Cefpodoxime200mg and Levofloxacin
250mg and also Anti inflammatory drug through mouth .
I do not think that there is relation between treatment of genital warts and clitoris enlargement
If it doesn't subside after 1 week,Consult your Dermatologist/General surgeon
Wish you speedy recovery