Heads, Intake & Carb upgrade...

IMO, at 5000 ft ( you didn't say),
that combo has the smell of disappointment written all over it, no matter what carb or intake is on it. The 3000 stall will not be a 3000 with that super low cylinder pressure, and so the combo is doomed from the start.

Something has got to go.
If the 318 has to stay, then I vote to ditch the Thumper, and get the pressure way up.
If the Thumper has to stay, yur gonna need more cubes..... with more pressure.
At 5000 ft, with the 318, you will need more than 11/1Scr with closed chamber heads to use that Thumper with a 3000 stall, and the 2.76s will have to go no matter what.
A 340 is not the answer for you, you are gonna need a stronger bottom-end.
With the Thumper, you will need a hi-Compression 360. You won't need all of the 3000, but the 2.76s still have to go.

But since your 318 has already been fitted with .030 oversize pistons, your cheapest solution is a small tight LSA normal type cam, or even, a solid flat tappet.
If you can get it up to 10/1 Scr , then you can run a 360 2bbl size cam with a 52* Ica
By 10.5 you can get the cam up to 56/58 degrees Ica
by 10.8 could be 60*
But getting over 10.5 is gonna be tough. Yur looking at a total chamber volume of less than 69cc. If the pistons are .054 in the hole that is 10.7cc right there! and the .028 gasket is 6.8cc, so if the pistons are flat-tops with no eyebrows, then the heads have to be 51.5 or less ............ so that's not gonna happen.
If yur heads are 60cc, then the piston deck clearance has to be less than
69cc less (60+6.8)=2.2 so basically at zero-deck. But if you gotta cut eyebrows then the volume is 2.8cc too big again. So 10.5 is tough.

But hey, if you are willing to give up some hi-rpm power..... you can slam those small-port closed chamber heads on a 360 and and keep the 2.76s with the 3000 and have a killer bottom end.

Lessee.
KB107s fall in at about .012 from the deck so that is 2.5cc and the eyebrows are 5 and lets go with the .039 fellPros at 8.8cc, for a total so far of 16.3.. Add in say the 60cc heads and I get 76.3cc..
Ok with a 20 over 360 at a swept of 744.6; this makes an Scr of 10.76! Badaboom! These small heads will pull to close to 5000, so lets put that Thumper back in, which is a [email protected] so also about a 5000 rpm cam. And the Wallace says, with an Ica of 52* , the pressure is predicted to be 156psi and the VP is a reasonably strong 135.
This combination will NOT make a lot of high rpm power. But it don't matter because with 2.76s, 5000 rpm will be about 53 mph in First gear, lol. Therefore 32 mph will be about 3000, and this is where the 360 will kickazz.

So there are your options; 318 with a much smaller cam. or
360 with the Thumper and 60cc (or less) chambers. You could use the 318 closed chambers. Or you could buy some aftermarket 57 to 60 cc big-port heads and get the topend back.

But you know, if I already had pistons in my 318short, I would just install a much smaller cam; that Thumper is just IMO a poor choice for high elevation operation in a small engine. As for me, I would install a short-period solid lifter cam/kit. And with a 318, those 2.76s would be long gone. And besides, that Thumper is gonna suck gas big-time.

Now, recall that I assumed an elevation of 5000ft. If you are not at or near 5000, all my numbers are meaningless. And I'd be happy to run the numbers thru the wringer for any other elevation, cuz I have a lotta fun doing it.

Lest you think me crazy for suggesting to run 318 heads on a 360, well maybe I am, but I did run early 318 heads on an early 340 once, with a 318 cam; and that was almost my most funnest combo ever,lol.
Woah! Thanks for the ideas! Are you a wizard or something!? Cool combo ideas! I do have a line on a 360 magnum for $600... Hmmm!