iPhone best options for restore

[dilly1066]

hi, i recently installed igotya app and it really messed up my phone, i had to do semi restore etc, ever since then im getting few errors in cydia, cant install anything from cydia, im thinking it needs a full restore, totally wiping, its a iphone 5, only shsh blobs i have are for ios 6.1.3, is there anyway i can restore it and then jailbreak it again ? i dont think there is and to be honest as long as my ipads jailbroken i think i be ok with iphone normal, only thing il miss is music box, anyway whats best options for restoring to original ios , the backup i have in itunes has fair few cracked apps on it, so they will fail when syncing from backup, ive got a back up of my notes and contacts threw ifunbox but unsure if i can use that on standard ios , thats all i want on after the backup if i can, would like a totally fresh clean start if possible, thanks