I was recently doing some recording with my stratocaster and was not getting good results. I was tweaking an amplifier at this time but after trying another guitar I found that my strat was just not sounding good.
I also have a Les Paul which is a VERY loud guitar. When playing the strat and Les Paul back to back I found the strat was almost louder than the Les Paul but not sounding very good. The strat is actually a guitar I put together from parts but they were all good stuff. It has a mahogany body and maple neck with a rosewood fingerboard.
The volume comparison with the Les Paul is what pointed me in the correct direction to improve the start’s tone. I had the pickups too high. You can get a good amount of output with the pickups close to the stings but the tone suffers. It sounded muddy and cheap. Pickup height is also hard to judge because all pickups are different. You can’t just look at the distance on another guitar and copy it. It really comes down to experimenting and using your ear.