1. What is a reasonable amount of money to spend repowering 36 year old boat?
First, there isn't
anything reasonable about sailing!

One book defines it as
"Sailing: The art of going nowhere, slowly, at great expense." We do this, not because
it makes any kind of economic sense, but because it is fulfilling and life enriching.
As for typical, I often hear a figure of around $17000 for a diesel repower. YMMV
($10000 hardware + $7000 labor)
Your cheapest approach would to go back in with an exact replacement, but unfortunately
the MD11C is pretty much at end-of-life, and parts are getting hard to find, let alone
a complete rebuild.
Your next best bet is an engine with the same mounting points, avoiding the tedious
and potentially costly need to modify the mounting bed. The only one I know who
has this is Beta Marine. They will make engine mounts to match your specification.
The 3-cyl Beta 25 is a good match for the 323.
When I did my engine replacement, I saved costs by doing most of the install work myself.
Its not hard, but you need good information and the proper tools.
2. I love her but I wonder if it's wise to go too far down this road... or consider alternatives. ..however buying another boat will certainly cost a lot more money.
Maybe not. The used boat market is incredibly soft. Seems that fiberglass hulls,
if reasonably cared for, last almost forever, so there is a huge glut of used boats on the market.