Welcome to the Forum. I'll try to provide some guidance but I think you really need to see another helath care provider, perhaps a dermatologist to sort things out. there is no current therapy for warts which are 100% effective. Both condylox and cryotherapy have about an 80% response rate so if the lesions were warts (visual diagnosis is sometimes incorrect) that the warts persist is not unheard of. Please remember that all of these therapies are essentially destructive, thus scarring may occur afterwards. When scarring occurs, it tends to get better with time.
Let's address your specific questions:
Question 1 - is permanent scarring what I am dealing with based on your experience with people receiving cryo for HPV or will it resolve in time?
See above, It should imporve with time. You might see a dermatologist . They often have therapy that can facilitate resolution o fscars.
Question 2 why is the condolox not clearing things adequately?
Answered above. No therapy for warts is 100% effective. This does not mean that you are abnormal or have particualrly treatment resistant warts.
3. If it is scar tissue which has formed rapidly (within two weeks) what can I do? Would rubbing the tissue help break it up? The presumed scar and remaining warts have put my sex life on hold and I feel very depressed about the whole ordeal.
This is rather rapid for scarring to appear. Scars tend to improve with time and increased manipulation may make it worse rather than better. I suggest you discuss this with a dermatologist.
Question (4) is around protocol for potential partners - should I inform all sex partners even if I wear a condom? What are the transmission odds? Is unprotected oral a no go? When am I safe to resume oral/full sex without informing partners?
In general we do not feel strongly about informing partners as HPV infections are so very common. Here is a link to another response by Dr. Handsfield that goes into detail:
http://www.medhelp.org/posts/STDs/Past-HPV/show/1814012
Question 5. Circumcision for this process is a bit dramatic. I would hold off and discuss with a dermatologist. EWH