What happens if you go to Kvatch before beginning the main quest-line

From the Oblivion Wiki:

Some magical effects can increase your skill above 100, but in general increases above 100 have no real effect. The only exceptions are Acrobatics and Athletics , which will continue to increase your character's jump height and run speed, respectively, up to a maximum value of 255.

As for attributes:

The current value of an attribute can be boosted past 100, and many, but not all, benefits of the attribute continue to increase for values greater than 100 (see Magical Effects on Attributes ). Most aspects of game play are based upon the current value of the attribute.

Fortifying an attribute temporarily raises that attribute's value by M points, for a period of D seconds. Fortify Attribute can increase an attribute above its base value and can even increase an attribute above the maximum value of 100. Increases in attributes past 100 have the same effect as below 100 with one exception: weapon damage. Luck's effect on other attributes of +5 Luck = +2 (Other Attribute) is not altered when Luck is above 100; however, as it effectively raises the level of other skills up to a cap of 100, Luck has a diminishing effect on attributes that exceed the cap, and ceases to have an effect on attributes that reach 100. See Oblivion:Luck and the other attribute pages for details of their effects on skills.

So while fortifying endurance past 100 will boost your health, fortifying strength past 100 will not boost your melee damage but it WILL continue to increase the maximum carry weight and fatigue.

Yes! Wrye Bash has a savefile browser tab that will show you a save's "master list", which is the list of mod files (and their order) that the save file depends on for all its object IDs.