wipeout is good at ruining a stock. To use wipeout, I and "paul company" recommends a bore guide, which alieviates issues as you are having. any of the aggresive bore cleaners will take off finish. You can't blame wipe out.

All you can do is find out what finish the stock has on it now. Sand the affected area with steel wool and hand rub in the finish no matter if its truoil, linseed, tung oil etc. Don't strip it. Unless you are experienced in refinishing stocks.