Going back to your first post
after a few minutes
the GPS receiver acquires enough sats to begin the 1PPS. At that
point the (10 MHz) CLK0 freq error will be several KHz. The
ATtiny84 controller will begin pulling the freq towards 10 MHz. The Si5351 Reg 2 can be seen changing the 27,004,xxx MHz as
expected. After another few minutes the Reg 2 value settles and
the CLK0 freq will be 10MHz +/- 2 or 3 Hz . But the CLK0 freq
will not remain at any freq for very long...just a degree or two
temperature change will start it moving and the Reg 2 value will
not change as necessary to correct the error.
This is expected if register 3 is left at default. have you set it to 0 when it has got near to correct? (Manual section 4.4)
The PPS is obviously working but it will not adjust correctly if the 27MHz drifts too fast. Have you checked that?
You have detailed a lot of redundant information, perhaps that has confused people.
73 Alan G4ZFQ