I did shoot more Sierras after using the JBs and the amount of copper pickup was the same. So I don't think the use of JBs nullified my breaking in the barrel early on.The only thing I would have done differently would be to not use the JB on the barrel if it was not fouling. You went to the trouble to do a break in and was getting good results. JB is an abrasive and by using it you defeated the break in process.
I would also recommend never making more than one change at a time. This allows you to see the change and the problem can be diagnosed easier, especially if you have a good load and just want to improve it. It is easy to second guess a problem but if you only change one thing at a time, it is much easier.
Also I have shot Speer hot cores and found them no worse than other bullets for fouling. I mostly used them for break in because they were about half price and reasonably accurate. Once break in is complete I always start testing with my first choice of bullets so I have a bench mark.
J E CUSTOM