Some more days later and 20 more hours of messing around with the canopy frame.
I've had it with this shitty piece of steel. I hate it by now. I ended up with a good match for as good as is possible.
In the images below you can see the rear bow is now reasonably close to the fuselage top skin. the front bow is also fine.

The next images show the side spacing while sliding back between the side of the canopy frame and the side of the top fuselage skin. This has to be an absolute minimal gap. If not, the frame will be too wide.
As you can see in the images, it barely touches the skin but passes without touching.

Something that worried me a bit is that the slider bar is slightly shifted to the left if you compare to the drawn blacklines which represent the sides of the bar when centered.

I decided to go for it and drilled the both canopy roller tracks to the canopy frame deck.

To ensure that the width front and back was exactly the same, I used a long scrap piece of aluminum from and check equal distance front and back.

The alignment looks nice and confirms what you see in the plans. Later on you have to grind a bit away of the outer side of the canopy track as it slightly overhangs the end on the side fuselage skin. This is normal ad the plans call for trimming here.

I also measured the distance from the side of fuselage to verify interference with the unerlaying top side of the longeron.

Before I drilled that hole, I had drawn the hole location through the pilot hole in the slider track with a fine sharpie pen.

I then put the right size drill for the final fastener on the hole location and measured from the side, you see that updrilling will not damage the longeron.

You will draw a lot of reference line on the top skin but in the end, it's really adjusting to your situation and getting the frame on the right height in relation to the top fuselage skin. You achieve this by moving the slider track back or forward.

Duct tape works well to keep it temporarily in place.

Drilled the first pilot hole with the final position. you see the hole is nicely centered on the slider track and the hole is a bit left of the center line of rivets on the top fuselage skin.

My biggest worry here was beingcentered on the underlying flange of the F-787 stiffener web.

 When looking from the inside, it actually came out pretty good. The hole is nicely centered on the flange which tells me the rivets are a bit on the inside of the flange of the F-787. A good coincidence that turned out well.

Also in the back, good edge distance on the pilot hole.

Only drill two pilot holes in the slider track and don't up drill or drill the others yet. You still have some playroom for final adjustments now and it's not the right moment to commit yet to these locations.

The frame will still be narrowed because it expands as much as an inch with the plexiglass bubble on. No way you can tell now if you can achieve to get the exact same measurements once the bubble is on.
So leave the pilot holes for now.

After drilling, I re-verified all measurements

Shape looks good.

Front bow relation looks pretty close but leg height will have to be final adjust later when installing the windscreen.

 Slider track looks good

Measuring from the fuselage side for the 1/16 inset from the sides looks ok

Here is my current height of the canopy frame on the slider track. I remeasured all distances after drilling and all looks fine.