Megasquirt is a aftermarket do it yourself fuel injection controller. It replaces the stock ECU, think Accell Gen 7, Big Stuff III, or F.A.S.T. but you build it youself. As far as the coil packs a lot of people move them to clean up the engine a bit. I love LS1's but I'd be the first to admit they are not the prettiest thing always. You can mount the coil packs remotely and run plug wires to them (looks like he mounted them on his firewall). Also as of yet there isn't any aftermarket coils for LS1's. A lot of guys run the truck coils as they are suppose to be a little hotter. Here's a little example of a '99 SS and you may recognize the valve covers as they are the ones I had made and posted recently and my buddy talked me out of them:
As you can see moving the coils cleans the engine up quite a bit. You can see the plug wires snaking back to the coil packs mounted under the cowl. As far as this engine, it is a bored/stroked 6.0 solid roller iron block that dyno'd 555rwhp/485rwtq (carrying 525to 7500 rpm) in 90+ temp and 90+humidity and this was N/A. The engine was built for nitrous, nitrous times to come.
And Rob I think that's a pretty good deal. Not absolutely great but if I wasn't planning on upgrading (heads, intake, cam, etc) I'd say it's worth it. Look at FirstGen's as nice, clean, stock looking example. Well, wait. Does it come with any accessories/brackets and throttle body? If not, no.