1/ With regard to the LTP grids, I'm not sure which you are referring to as being inverting and non-inverting?
How about g1 as the main input grid, g2 as the feedback grid, as per Merlin's page The Valve Wizard -Long Tail Pair
If scoping g2, bear in mind that it's inside a negative feedback loop, and so what you are seeing is largely the error signal.
If scoping the power amp, it's much more helpful to open the feedback loop.
2/ I suspect that the LTP was designed for a 12AX7, and for some reason a 12AT7 was swapped in, with pleasing results. Perhaps the lower gain made overdrive less harsh.
3/ Not sure whether you are referring to the LTP bias (eg 470) or tail (eg 22k) resistor?
4/ Grid stoppers should be fine.
5/ Very high values may act with the tube's Miller capacitence and roll off HF at too low a frequency, perhaps making the tone dull. Also they add to the total grid-cathode resistance, which may then exceed the limiting value. Off the top of my head, I suggest 22k as a max.