I think you should have a look at http://www.tesnexus.com/downloads/file.php?id=11495. It starts off doing precisely what you want to do: dropping the player off at the Anvil docks to start the game, and re-rigging the MQ to give the player more leeway on starting it. You could either learn from it by example, or just use it, in the case you don't go forward with your own plans.
I am pretty sure the stuff you are doing right now is game-breaking, unless you are also planning on rebuilding the main quest & all the oblivion gate quests & all their scripts to account for all these deleted objects (which are referenced by those quests and scripts). I don't want to deter you in any way, but I am sensing a dangerously wide gap between your existing modding knowledge and what you'd need to have to make this sort of mod. It is the kind of project that would make any novice punch walls and give up (perhaps not just novices). Not simple at all, at least in creation, as your topic title implies. If you already know what you're doing, please ignore everything I just said - but otherwise, please save yourself cumulative weeks of frustration by going through the tutorials to learn some mid-level modding stuff, like quest building and some basic scripting, before attempting this.
All that said-
There are placeable sounds, yes. They are found under Misc. in the object list. In the CS render window, they look like little red speakers. Open the cell you want to remove a sound from. In the cell window, you'll see the list of references contained in the cell you're in. If you can't see the sound in the render window, check for it in this list. Double-clicking it from the list will bring it into view; alternately, you can right-click it from the list to get a context menu. If it's not in the list, then it could be that the sound you're hearing is attached to a light or activator that is still in the cell.
For your wayward NPCs: Find them in the object list. Right click one, and choose "Use Info" from the context menu. That will list for you all objects that refer to that NPC, including scripts and quests and cells. Double-clicking a cell from this list will load the cell with the NPC in view. You can do this for any object, not just NPCs.
And erm, as I've said, I'm pretty sure you've broken a lot of things. Whether or not those casualties are acceptable or not will be up to you, of course.
Character creation is only three script commands. "ShowRaceMenu", "ShowBirthsign", and "ShowClassMenu". Peek at the mod I linked you to see how to use them.
Good luck!