your as-is numbers are not bad on CW. (some of us would gladly trade board with you - actually mine is somewhat simpler - except I had an even larger dip on 40m, that I corrected with a capacitor change pointed out by Asshar). remembering each S-unit on receive is approximately 6 dB - I would not myself want to change anything. (if you really really want a flatter PA - you could possibly buy the 10 watt PA kit from QRP-Labs, and use it instead of this portion of the ubitx - but funny thing when we get good solar flux in 4-6 years from now - you might be using a uBitx v12 or a QSX v3 ....)
SSB needs to be evaluated separately, using an audio oscillator as an input. the SSB path uses the 45 MHz mixer 'as a mixer.' CW is different because it puts a bias onto the mixer, and then leaks through a signal at the intended RF (no mixing!).
keep in mind the driver and PA are common to both CW and SSB - the overall behavior should track but you may experience different degrees of dip and peaking. with the circuit board as is - you can only do so much with the overall behavior of the PA and tweaking of the driver frequency response. you might work very hard to get a better measurement into your power meter on 40m that the operator on the other end will not even notice.