What do you mean for "Clearer"? Class D or PWM amplifiers has an intrinsic limit in the frequency they can amplify, give certain switching frequency, the high part (treble) of the spectrum will become more and more distorted (like metallic sound) as the frequency approach sample or frequency of the PWM. So you can't enhance the high frequency response without limit. (Limit is about Fsw/10).
"allo.com" has a TPA3118 version that is probably among the ultimate uses of TPA3116/3118. You can get some ideas from their design. An improved output filter is one possibility. TPA3116 is amazingly well sounding for the price but it is not in the top of the chips from TI.
Treble control or an AMT or planar tweeter?
Tube T1 preamp with tone controls and you can also try tube rolling
What speakers do you have?
What ampboard do you use, countless times tubepreamps are used by people who want their 3116 to sound warmer, I don't associate that with more clear, sorry.