1) Digging Equipment An experienced operator should be able to dig that pond in way under a day depending on access. Normally the most economical machinery is the largest that can get in and out in about a hour. But an experienced mini excavator person can beat an inexpereinced backhoe person. How long will it take you? Don't know. A neighbor once rented a Bobcat to redo his yard. About 6 hours of everyone doing donuts, and maybe 12 extra hours repairing stuff that got ripped up by mistake.
One person on the excavator and one on a Bobcat moving the dirt is about the fastest.
Hammer drill works great but is a manual deal. I'm strange but I like digging by hand. Time to think and a good workout.
2) Bottom Drain
Bottom drains are really about O2 management. Debris uses O2 decomposing and high end Koi keepers want all O2 going to their fish. Plus many of those ponds are right on the O2 edge so O2 management is absolutely needed.
In a Water Garden O2 is rarely even close to being an issue. These kind of split the difference muck wise, some people being OK with it, some not. Most bottom drains I've seen or read about in Water Gardens weren't really bottom drains imo. A bottom drain to me has to have a way to flush debris to the drain, missing from many Water Gardens.
In Wildlife ponds muck on the bottom is as you described, a necessity. Here it is considered a bio filter while in other kinds of ponds it's considered toxic by most keepers.
Sounds like you want more of a Wildlife pond than a Koi pond so muck is good. You can even add muck to get a jump start.
3) Stones
I thought stone was cheap here, $4/ton for pea grave is unreal. 10 tons sounds about right, but of course it totally depends on the pond.
The different size rock does provide an instant perfect look. However, my personal choice is to mortar rock over the liner as a base even in a stream. A few loose rocks can be added as needed. The reason I prefer this is maintenance. Dog digging in the stream, no problem. Kids, no problem. Need to clean, less problem. Messing around with plants, less problem. And over time loose rock moves around and doesn't look as good as the first day. With the mortar I can get that natural look and have it stay in place.
I prefer mortared rock bottom for looks, protection, and easy cleaning. But I might not bother with that in a Wildlife pond and just do the sides. But that's just my tastes.
Can't wait for pictures of the dig.