This last thing about confusing the player in a dungeon may be frustrating, but as I like messing around with players/readers/listeners in my art, (counting literature, music, and video gaming as arts) I'm for this all the way. Except that you should please give away some way some way of deciphering the map. It can be as cryptic as you want. Just make it there
As for your other things:
No Fairy Fountains
I don't mind. I never use fairy fountains in my quest, and basically never usethem during gameplay either. I'm having life shops instead. And my enemies drop hearts. However, this means that your...
...enemies don't drop life (or magic?)...
...would be extremely annoying. And I guess life shops are just fairy fountains that you pay for. So neither would be viable with both of these. at least make enemies drop some life. It doesn't have to be much.
Enemies drop less rupees
Only if you need less rupees. As so many have said, people don't like to grind.
No clocks
Completely for. I need to remove the clocks from my quest.
Link only starts with 3/4 of his life, except at the beginning. Heart containers and pieces refill life.
This may be annoying, but if you have a quick way of healing near the starting point, then go ahead. Like in aLttP, where you started with three less hearts than max, but in your house, there were three pots, with a heart beneath each.
Except now I realise you said 'heart containers and pieces refill life'. If you're doing that, then make them numerous. Make there be a lot of heart pieces and containers. If not, people will get annoyed.
No F6
If there's another way of saving, go ahead.