LS1 honed to like a 3.903 or 3.905 somewhere in that area, with a stock head gasket and 241's what would be my CR? i would like to bump the compression up a lil bit and have some better flowing heads at the same time and not get out of the quench area. i was thinking of using a 317 milled .045 and a .045 gasket, would this work or would i loose compression

 

Using heads that are milled more than .035 will hurt your flow and negate your potential compression gain.

If budget is your game, then mill the 241s .035 and get them ported. However nowadays you can get a set of ported 243s (LS2/LS6) stage 1s (with LS6 springs) for
less than $1000 (flowing ~300cfm intake)

 

how should the LS6 Stage 2.5's perform (2.04 & 1.575)

 

From who, PRC? (only because they carry stage 2.5 with same valve and your cam is 228r)

Only use 2.04 if they have aftermarket seats. 2.04 on stock 2.02 seats is a sales gimmic, not allowing full potential of bigger valves.

If you have the $$, then the 5.3L PRC with 2.02/1.57 valves will be nice with the 228r

 

i got all this from TSP website

 

How does milling the cylinder head hurt flow?

 

Because you are shrouding the valve as you are reducing it surrounding chamber area. This is more true with OEM casting VS let us say AFR because the AFRs have thicker decks and deeper chamber shapes.
This effect is also increased as valve size increases.

 

Yeah, but in this case isn't the chamber on the 6.0L head is for a 4" bore but going on a 3.900" bore. I don't think .035" mill is enough to shroud the valve anymore that what the bore is going to.

 

He is milling .050 not .035
Not only that but he might have intake allignment issues.

The proper way to reduce chamber size in 6.0 castings is to weld the chambers and reshape. to desired volume.