If you're using Iris chain or D.I.D. ZN2, be aware that these chains are waaaay more durable than the cheap stuff. You won't get much stretch, so be careful you don't make it too short or you're basically screwed. I've seen about 1 tooth's chain stretch (1/2 link) after 2000 miles. Assuming you know what size sprockets you're going to run, a test fit is the only way to determine the best chain length. There's roughly 3 teeth worth of adjustment, max, in the rear swingarm axle mounts and no half-links made for these chains. Ideally, you'll get the needed length with the rear axle in the front half of the adjustment range. If you end up with the axle near the end of it's travel, then you may have to live with it. If the chain does elongate more than the adjustment can cover, then you'll be able to remove a link at that time.
Splice orientation is a moot point. These chains have their own specific master links because the links themselves are wider. Just orient the spring clip so that the closed end faces the direction of rotation and you'll be fine.
I prefer to grind the pin ends flush with the sideplate and drive them out with a punch. It is also advisable to remove the excess lube from the outside of the chain. The heavy grease used by the manufacturer will attract sand & grit like a magnet and the first time you hit "the dusty trail" you'll watch the chain suddenly "stretch" within very few miles (it's also murder on sprockets). Mineral spirits & a rag or aerosol spray dry-film chain lube work well for removing the excess from the outside while leaving the pins & rollers lubed internally where it really counts.