not to insult anyones intelligence here, but where the hell are you guys coming up with this stroke crap?
no, it does not matter what stroke the SHORT BLOCK is in when you time the cams, If you have found a proper TDC for #1 cylinder, and installed the timing chains with the marks lined up, you will be fine.
then you need to do do the same thing for cylinder #6 for the drivers side. once you find that TDC, and line you cams up accordingly, theres no way you could be on the wrong stroke.
turning the shortblock over by hand while the heads are off has no effect on final assembly, think about it, if you found TDC for say your compression stroke, with the heads off, and turned the engine one complete revolution so your at the TDC of your exhaust stroke, one full revolution of the crack is gonna put all the piston exactly back where the were.
your crank position sensor, and cam position sensor determine what stroke the engine is on. the PCM gets a signal from the Crank trigger wheel, and the driver side cam gear, once it knows that Cyl. 1 is at TDC, and the intake valve is the next event to open, it fires the injectors, then spark, then moves on to the next cylinder.
so in short, if you have stock cams, or "stage 1" cams, you can just slap em in with the timing marks on your gears and be done. if you have a "stage 2" cam or more, you need to degree them. they will be around the factory marks, but not dead on them. if you are installing a small cam, or stock cams, and want to feel good, rotate the crank by hand, make sure it makes 8 full revolutions, and if you feel any resistance, stop.
hope this helps.