For point 1, I've had a few more thoughts about the possible reasons for doing that level of detailed clean-up, which are in my reply to ShatteredSanity's comments below.
I agree, actually writing out such a search would make for dull reading, so I'd probably just try and handle it with some dialouge once the agents were back in their RC, for example:

"Three hours! Three hours spent searching through that damn forest, just becuase 'Litte Miss Speshul' dropped her iPod."
"Well, would you rather waste three hours, or go ask the SO for a different punishment?"
"...the searching, I guess. But next time I'm bringing a metal detector."

For 2, cool; that question arose from a fic I read (can't find the link at the moment, but hoping to retrieve it for use as a future mission) that had a Sue that was so speshul she could stop bullets, with her mind, as opposed to the more traditonal method of body armour. She was also an ace gunfighter (obviously). I figured one of the best ways of dealing with her would be a surprise attack; one agent up close to read the charge list, with the other a long way off with a high powered rifle. Can't stop a bullet if you're not aware of it.
Sniper rifles should be OK in the canon, becuase just about every other type of gun is there, and there's no reason (that I'm aware of) that snipers couldn't exist in the setting.

I'm glad that I can use a Beta for my permission piece; I thought that'd be the case, given that this community is all about writing well. I wanted to make sure of that before actually asking for a Beta, just in case the permission piece was meant to be solely what I could do myself. Thanks for the link to the list of Betas.

As for point 4, I'll make sure to tag my claim as pending (as soon as I actually get over my nervousness and dare to make changes to the wiki). Regarding the OC, yeah a couple of canon characters that should know a lot about magic are surprised at the strength/ability displayed. I'm fairly certain now that this is indeed a Stu, which means that the agents I'm working on can find a home in the DMS.

Thanks again for your help.

First off, I think I may have missed your introductory thread, so just in case; hello and welcome!

I'm currently in the process of proof-reading my piece, and glad that I did so before starting to look for a Beta. Some very odd mistakes seem to have crept into it while I wasn't looking.

Regarding 4, now that you've mentioned that, I seem to recall something along those lines too. As you say, the SPaG alone makes it a worthy target, and I'm looking forward to being able to send my agents in to deal with it.

Thanks for your help; any opinions are useful.

Yeah, I'm often unsure whether or not to try and answer any questions posted here, seeing as I'm so new, but everything you've said makes perfect sense to me.

With regards to point 1, a personal theory that I'm working on (which one of my agents will probably hold regardless of whether it's actually true or not), is that after the all the major stuff has been dealt with, the canon can handle the little stuff. But that the way it does this is to absorb it, so the actual object disappears from view, and can never be stumbled upon by any of the canon characters, but it forms a sort of 'narrative cancer' that still damages the continuum. The more 'cancerous' it gets, the more outside stuff has to be removed before the canon can reassert itself. So by cleaning up as much as possible, rather than just as much is required, it's possible to keep the canon 'healthier' and stave off the time where it becomes necessary to remove memories and skills as well as the physical artefacts.

I'll probably just have one for two favourites that they obsess over cleaning up as much as possible, but deal with anything else in the normal way.

With 2, there is a slight difference between the worlds of Harry Potter and Trigun, in that HP is set in the real world, with a twist (in that magic exists), so anything available in the real world would be available in HP. With Trigun, they're on a different planet, so not everything from Earth is necessarily going to be available. But I think that seeing as how every other type of weapon seems to be there, the concept of a sniper rifle should easily exist, and so the canon shouldn't have any problem with the concept of sniping a Sue from half a mile away.

Thanks for confirmation on the Beta's.

With 5/4, I was fairly sure it was still a Stu, but wanted to check as it's going to be my first mission. Wouldn't have wanted to have written up a couple of DMS agents, sporked the fic, and then have someone say 'That's good, but it wasn't actually a Sue/Stu, so it'd probably have been better for agent from the Department of Floaters to deal with it', or something like that.
With regards to the editing; that's exactly how I feel. I mean, it's just text, so surely there's a limit on how complicated it can be, but I was just looking at it thinking 'what if it all goes horribly wrong?' Still, if I don't try it at some point, my only other option would be to pester people on the board to do it for me, and I imagine that would get annoying very quickly.

*goes away to contemplate that fearsome 'edit' button*