First off, this project is using a non-standard grip,
Which uses a non-standard screw.
Hence the questions about approximate standard fitment.

When fully seated, does the grip screw protrude beyond the top edge of the grip?
If so, how much so?
(Wondering if I need to shorten the screw,
as it sits about 1/4" beyond the top edge off the grip)
So I want to make sure it won't get in the way of fire controls.

Second issue
The shoulder bolt isn't threaded far enough to match the bottom flat of the grip.
So I may need a tap n die to thread it another 1/4".
Why all the work?
It's a old colt furniture set that has a non standard grip and screw set up
And it came without the dang screw.

I've used shorter 3/4" 1/4-28 cap screws in place of the standard grip screw (1 1/4" IIRC). You can just try one first to see if you have enough clearance. I use the 3/4" with a 1/4" set screw to adjust for over travel. IIRC the std screw is 1 1/4".

Generally the upper end of the grip screw will not protrude into the fire control cavity of the lower.

You can always use washers under the screw head, if it gets too out of hand at least you have an accurate measure of how much to shorten the screw. I wouldn't die it, just get a replacement that has a longer thread length.

And no, it shouldn't protrude into the fire control cavity at all.

screw is 1/4-28 x 1"

The grip screw does NOT go into the FCG area. In fact, many lower manufacturers don't even fully thread the grip screw hole (such as Anderson Manufacturing).

^ why is that? I discovered this yesterday and trimmed the grip screw to fit.

I have no idea, and it IS annoying (as I use Anderson lowers). However, I use Magpul K2 grips exclusively and they come with a short screw that works with those lowers (BARELY. The grip finally runs out of play just as the screw bottoms out of threads). It's the only gripe I have of Anderson lowers. Other than their refusal to finish threading the grip screw hole... they are GTG.
ETA: there was a huge thread on here not too long ago on this topic. Anderson recognized that these SHOULD have been fully threaded (per mil spec), and offered to "finish" threading customers lowers... but still has not changed their ways (new ones are STILL not fully threaded).

When it extends into the fire control pocket of the lower it may contact the rear of the trigger and produce undesired results.  A .750" or 1.00" long screw should work just fine.  That is why some manufacturers do not thread the hole fully.  The "short" threads will stop the screw before it reaches the trigger.

The problems that I'm running into.
Because this is not a standard A1/A2 grip,
A standard 1/4 x 28 x 1 bolt, is 2" too short.
Also, the hole for the screw is barely wide enough for the bolt itself.
No room for any washers.
So why not drill out the grip?
A: because it is a rare factory colt grip
Why not use a different grip?
A: because is part of a complete set of original colt furniture
(that is sadly missing a key bolt)