AI've been trying for weeks to figure out how to throw this project idea at Henry D. I also want to step up our stocker/bracket wagon, and I was looking to swap an LS-based engine into the engine bay. Thanks for giving me a reason to throw the pitch. It's a great idea, and yes, the aftermarket has really stepped up with rotating assemblies, valvetrain, cylinder head, manifolds, and so on.
You could make front engine plates that would sandwich between the water pump and block. Compared to a small- or big-block, it would be a little tougher. The LS engines utilize three bolts per side and are 8 mm in diameter. These are slightly larger than 5/16-inch fasteners. Making killer power held in by three 5/16-inch fasteners per side doesn't cut it with me. I would make up side mounts off of the factory mounting pads on the side of the block and bring them forward to the front of the case with a 90-degree flange. Then you could attach front mounting plates to something much more secure.
Don't worry about the one trans mounting bolt hole on the right upper location. It may be because of a head bolt location, but it's because GM reduced the rear flange depth of the block by 0.400 inch. When the LS family of engines was being developed back in the middle '90s, they wanted the engine to be as short and compact as possible. The rear of the block is as flush as they could make it compared to either a big- or small-block. We've run without that upper bolt hole for years without a worry.
You also mentioned that the aftermarket has stepped up to SFI flexplates, flywheels, and converters. The crankshaft flange is also moved forward 0.400 inch in relationship to the bellhousing flange compared to a standard small- or big-block. If you wish to use all new components, that's great; but if you want to do it on the cheap, use crankshaft spacer PN 12563532. This makes up the 0.400 inch of deficit in crankshaft length. You must also use longer bolts, which are sold under PN 12553332.
Finally, there are a couple ways to skin the ignition issues. The cleanest by far is the GMPP LSX controller PN 19171130. This is a standalone computer and ignition system that utilizes all the factory sensors to feed it the proper information to feed the eight-coilover-plug ignition. This small little box features programmable low- and high-rpm rev limiters, custom advance curves, and a step retard that you are able to program with the software supplied. This kit comes complete with box, wiring harness, and software. This makes it a no-brainer to plug and play any LS-based engine.
MSD also offers two ignition systems for carbureted LS-based engines. The 6LS has all the same features listed above except for the wiring harness. MSD says with a handful of connectors you can use a factory harness and wire in this controller. PN 6010 is designed for the 24-tooth reluctor wheel and is for LS1/LS6 engines, and PN 6012 is for the 58-tooth reluctor wheel and is for LS2/7 engines. If you're stuck on using your MSD 7AL3 then you need the LS front distributor drive cover. This is an adapter front cover that mounts a distributor and mechanical fuel pump off the front of an LS engine. It is sold under PN 88958679. One of the pains of using this setup is that it requires you to use a small-block-Ford-style distributor and mechanical fuel pump. It also requires you to use an aftermarket damper.