First time post engine rebuild advice please

I think in your case you have already addressed the biggest down side. You have better pistons in it so you can play a little more. If you are running a milder cam profile, which is what I'd suggest, I think the 360 heads with the 1.88/1.65 valves, a .030 mill, and a performance valve job would be fine over doing any special prep work on the 318 heads. There will be a bunch of other ideas. But that's mine. There is much to be said about over thinking a basic combo and I think with the lower end done you are head and shoulders over someone with a stock piston.