Morse Y2D | Standard v Drop Tune | Pickup Question

Firstly, apologies if the title of this thread is a bit confusing. I will try to be as clear as possible with words that follow:

I have a Morse Y2D and it’s a great guitar in terms of ergonomics – love the body, bridge design, and the neck. For the longest time, I’d strung it up in standard tuning using 9-42 gauge strings. Truth be told, the tone was good, but personally not the best for me. I’ve realised that I like the all mahogany construction (Neck and body) with sightly shorter scale for my standard tuning fixed bridge guitars.

Hence, I strung up the Morse with 11-52 strings and have tuned it to C standard. Honestly, I love how the guitar feels with a low tuning and the great ergonomics (including 25.5″ scale) certainly help. However, there’s a problem with tone.

I like how the guitar sounds clean but with overdrive, the mid-heavy pickups really don’t work at all for overdrive or heavy tones. So here’s my dilemma:

Is there something I can do to get the Morse to sound closer to the shorter scale all mahogany construction sound or should I keep it in the C standard tuning and look to replace the pickups?

Would appreciate some inputs on this.

Thanks!