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So I'm essentially thinking/attempting to recreate 40k in some kind of vain attempt to balance things I don't like (likely only to ruin others).
Its more of a project for me than anything else (so house rules).

I was contemplating the idea of making changes to weapons and thought about some of these:

Maximum Range
Optimum Range - weapons can shoot in this range with no penalties and/or some bonuses e.g. melta gets a bonus to shooting in close (like present) or weapons shot outside the range are BS -1 or -2

Re-purpose Rapid fire to be equal to assault weapons except they cannot be used on the charge

So a bolter could be S5 (assume this is the average strength for now) Optimum 24" Rapid Fire 3.
A Pule rifle could be S6 Optimum 30" Rapid Fire 2

Also looking for some ideas about AP.

I was thinking AP could affect armour by a certain amount but not sure how to best implement this.
Maybe a table or something and ideas?

If you go digging you will find a number of similar projects floating about on Dakka (my own is linked to in my signature). As to your suggested adjustments to weapons I know I used to-hit modifiers the way WHFB did (up to half range no penalty, outside half range -1 to hit, among other things); it went in as an entire system to replace everything 40k would call cover saves. As to AP I implemented that as a penalty to the target's armour save (so a Terminator with a 1+ save getting shot at by a heavy bolter with AP -2 has a (1+ goes two steps back to 3+) 3+ armour save).

IMO the modifiers to hit could simply be .

Target in light cover -1.
Target in heavy cover -2.
Target over 30" away,(Long Range.) -1

AP values could simply ignore save rolls that roll the same or higher.
EG AP 6 ignores all natural rolls of 6 to save.

Inv saves could ignore the AP value of weapons .

EG a terminator with a 2+/5++ save.
Is hit by an AP 3 weapon.
Normally they would only save on a 2+,but the invunerable save ALWAYS works.
So they save on a 2,5 or 6.

This has the same effect as armour modifiers ,but uses more familiar values.

You've suggested that save system before, Lanrak, we pointed out to you then that it's mathematically identical to save penalties and visually harder to discern on the tabletop. It'd slow the game down more and do the exact same thing.