Hi
Stuff happens to all of us. It depends on how well we deal with it.
Re. hay pokes - perhaps looking for soft meadow hay will reduce the risk of hay pokes and things sticking in noses? It can never be fully eliminated; a romp in the hay is important enrichment.
Cysts in the skin happen; they are generally down to a genetic disposition (as a re fatty lumps) and they are pretty common, especially as piggies get older.
It is estimated that around 70-80% of all sows develop ovarian cysts throughout their lives; thankfully it is actually a minority that causes serious trouble. The vast majority goes unnoticed.
Sows: Behaviour and female health problems (including ovarian cysts)
Not all forms of sterile IC seem to be easy or straight forward to treat or may be caused by something else. There is unfortunately only so much we can do. At least we can do more now than at first but medical research and progress is a slow and tortuous progress, and guinea pigs as a pet species are sadly a long way down the queue...
As long as the symptoms are minor, you may have to live with it.
Once you have excluded skin parasites and fungal, itchy skin is not easy to treat. Perhaps a dip with malaseb could help? It is antimicrobial. You may also consider whether the humidity in the room could play into it. Some teddies do have a genetic link to itchy, dry skin with thinning of the hair as a breed specific problem with the vernacular name 'teddy skin'. There is nothing you can do about that, as I can testify myself.
All of that doesn't make you a bad owner.
You can hopefully do something about the hay but most of what you are reporting are the kind of issues any owner comes up against sooner or later with their pets.