These are excellent questions and I will contemplate the answers and post them when I have more time. Just wanted you to know that I'm considering them.
Thanks first of all, I was under the impression that I just needed clarification with my questions. Since that is not the case and my questions are some that you need to contemplate before you have a answer ready for them, allow me to give my own suggestions for the three.
1 - I took a que from the diseases and it seems like the "improve" Endurance DC is about 20 + ½ level. This might be a little high for a 1st level character with 8 Con, so either reduce it by 1-2 points or he/she will need the aid of a character with high Heal skill.
2 - (Not sure here, as this was a clarification question)
3 - The easiest here is to take it by the letter and only have a characters own healing surges suffer (this also seems the most obvious, as the clerics magic shouldn't be dampened just because another character is wounded).
After reading the last couple of posts, it got me thinking though. There is a certain "death spiral" as
Vyvyan Basterd mentioned, which slows the game. The problem with many wound implementations is that it will make the character kill the opponent slower (in the case of penalties for attack and damage), which means he/she might take more damage or healing is penalized (which uses up more healing surges). Both makes the party end their day earlier.
Another way (which might already have been suggested) would be to not apply the wounds until after an extended rest. Consider it as though you wake up the next day, the adrenaline of the previous day has faded and now your wounds start to *HURT*. It might not be as realistic, but once the party is taking their extended rest anyway, taking a couple more in a row will usually not have a great impact on the game, whereas being hit with penalties during combat or when taking a short rest would make the players want to go back to town and rest up. This can also come at a bad time, when the players are in the middle of infiltrating the enemy base.
Of course, this also removes the interesting element where players might have to suffer these penalties because they have already snuck into the lair of the bad guy and taking a longer rest is not an option. But if the reasons for implementing wounds is simply to give the players some natual stopping points (like any sane person would after fighting a dragon), then this might be the way to go.
A last point I'll make, and then you shall be rid of me. Obviously, these wounds need to have a certain penalty associated with them, no matter if they are applied right away or the next day. I am not a big fan of penalties, as it is my experience that players tend to forget the -1 or to reduce the amount healed unless it is recorded on the character sheet. Since they are meant to be temporary, that shouldn't be needed - but alas, I can come up with nothing better at the moment.
I really like the idea of wounds however, especially as a way to give characters (or NPC's) distinctive scars, so keep up the good work!