"I put the little hose out of the water pump cover and the hose from the back of case into my soapy spray bottle I didn't see bubbles"
OK, you did good. Now you know the crank seals not leaking.
OK, now I see the bubbles. Like I mentioned, it's perfectly normal for the bolt holes to be drilled through. However, you need to figure out how the pressure is getting into the bolt hole. Did they port the inside of the reed box too much?
So, the air leak is on the left side? Wasn't it the right side that burnt a hole in the piston? Looks like you need to keep looking for the problem. However, on an equally lean condition, the right piston will usually burn a hole 1st.