As you mentioned, the PLL data checks out on all channels. Verifying the math: On ch1, N=143, and since 10kHz*143=1.43MHz, your measured VCO frequency "should be" 11.11166666*3+1.43=34.765MHz on AM. With your 11MHz crystal off 306Hz like that, the VCO would come out to 34.76408MHz. That's 1kHz off, not 10kHz, so that's not the only problem. Moving on.
Your clarifier varies the VCO from 34.75588 (left) to 34.7705 (right), and our target is in between those two values, so that's working fine. That clarifier range seems a bit wide for use in a SSB radio though, but the correct frequency is within that range (even if its not at the center). Side note, you don't want that much slide on a sideband radio, it makes setting it right really hard in SSB as mentioned in the first few replies to this thread. Still, not the only problem, moving on.
Since the 11MHz error only accounts for 306Hz*3=918Hz total, we still need to explain away the other 9kHz worth of error. The only explanation would be at the 7.8MHz oscillator. You didn't measure that in AM, only in LSB and USB. Is there any reason you didn't measure it in AM? Hint: L17 is only switched in during TX, so you gotta key up for that one (and set it for 7.800).
Can you share your alignment procedure? I don't have the sams for this and I just want to see if there is something in there that might be the cause, like something tuned in the wrong order.
The fact that the clarifier makes the oscillator drop out is also a hint that something is wrong there. Did you put the correct trimmer back in? Is C152 missing? When the varactor voltage goes up, its capacitance drops. If there is no parallel capacitance, it could very well cause the oscillator to drop out from insufficient capacitance (too much reactance in series with the crystal). I suggest putting it all back to bone stock until you get it working. Then modify.
Go check out the 7.8MHz signal in AM TX and let me know what you get.