The LQ4 use the same valvetrain, heads, block, and crank. The difference comes in with the pistons (and possibly rods). The LQ4 used dished pistons to give a CR of 9.4-1, while the LQ9 used flattop pistons to yield 10-1. Its been rumored the LQ9 had stronger rods but thats still up in the air. The LSx bottom ends have been proven to 500-600rwhp without any work. A simple oil pump and rod bolt upgrade goes a long way. The crank is usually the last thing to be replaced and can take a hell of a beating.
The heads on both are '317 castings. They have the normal cathedral style LS1/LS2/LS6 ports. They flow very close to the '243 LS2/LS6 castings but have a larger combustion chamber to lower the compression. The LQ4 is a good canidate for a power adder because of its lower compression.
The 90% of 6.0's around are LQ4s. You will pay quite a bit more for an LQ9. I bought my LQ4 for $1350 with 40k miles and all accessories (cheaper side around here). The cheapest LQ9 I could find was over $2000.
So the power difference is purely because of the compression range.
The rectangle port heads you are talking about are found on the new L76/L92 6.2 motors. They flow 325cfm bone stock, just about the same as LS7 heads. They are honestly the best deal right now for a set of heads, only downfall is they need a 4.00" min bore size as the valves are huge with an offset intake rocker. The 4.8/5.3/5.7 guys can't run em. I've seen them first hand and they are works of art.