I've been sitting here on the sidelines for a while. I was hoping to have a complete solution finished by now. However, life gets in the way. I unexpectedly got 2 consulting jobs, plus my teaching job has eaten up most of my free time. However, I think it is worth putting my 2 cents in now.
I will address the harmonics issue. We need to look at the root cause of the problem. The harmonics occurs in CW because it is direct conversion (or no conversion?) CLK 2 runs at the operating frequency. This clock comes from the infamous SI5351 chip that is also causing the spurs. Well, this clock is a square wave. The mixer it drives is unbalanced in CW and the clock just passes through and goes through a lowpass filter. (L1-L4 etc.) This removes frequencies above the 10 meter band. As most of you know, a square wave is made up of only odd harmonics, so we have the 1st, 3rd, 5 th etc. harmonics coming out. So for the 80 meter band operation many harmonics will pass through this lowpass filter get amplified and need to be filtered out by the output lowpass filter. We see fewer harmonics from 40 meters, mainly the 3rd since the others are removed by the first lowpass filter. At 20 meters and above the signal coming out of this filter looks like a sine wave, it has all the harmonics removed, hence there are no harmonics coming out of the transmitter. Garbage in garbage out. There are many ways to solve this problem. To date most everyone has blamed the poor output filters. We could also fix this problem by insuring we always drive the transmitter section with a sine wave to begin with.
So, we could modify the L1-L4 so that its cuttoff frequency is about 8 MHz for use on the 80 and 40 meter bands and stays what it is for the other bands. This will remove the harmonics earlier in the chain.
Another, easier way is to heterodyne in CW as well and go through the 45 MHz filter. So we need to move the unbalance circuit from the above mentioned mixer to the CLK1 mixer. Drive this mixer at 45 MHz and clk2 would would be the same frequency as we use for SSB and the harmonics would be gone. To do this all we need to do is lift R105 and so it stands up on the C1 side pad and place a jumper wire from the open end of the resistor to pin 6 of T4. Of course the software needs to be updated, but now without any filter changes, and with a very simple hardware change the harmonics are history!