I can relate to the OP somewhat. When I bought my first bike my LBS fitted me a certain way. Didn't like it and I did all the wrong things trying to get it to fit. Swapped to a shorter stem, moved the seat forward, etc. Felt ok on short rides but could never get fully comfortable on 2+ hour rides.

I then found BF and started reading fitting threads to understand riding position, weight distribution on the bike, etc. I then used the comepetive cyclist fit calculator and moved the saddle back a bit, increased the reach and drop and now I can ride forever comfortably and faster too