Couple of questions about a 426 heee-my in an A-body, if anyone has experience:

1) Offset master cylinder: Will the driver's side valve cover clear with just the offset MC bracket or does one need the flexible brake lines to facilitate removal so the VC can be removed?

I would use flexible lines. You didn't say whether you had a solid or hydraulic cam. With a solid, it is a no-brainer. But the flex lines make any necessary under-valve cover maintenance a lot easier.

2) Pass side shock tower modification: Cut and sectioned, or a 20# sledge hammer ala the factory. Is that for VC removal or complete head removal ability?

What do you want it to look like? Certainly, cut and trim looks better than bashing the thing in, if there is even enough room to just bash it. We had to move the top shock mount over nearly an inch in our Dart. It is best to test fit the engine and see what HAS to happen to get the monster in there.

3) Where is your alternator when using a motor plate or "Elephant Ears"?

Thanks in advance!