Some strange behaviors in Mountain Lion

I was going to do some of the things you described, but then I noticed something interesting in my system: After I installed the 10.8.1 update, a file got dumped onto the top level of my hard drive. It's labeled "mach_kernel" (without the quotes), and I find it a bit disturbing that it got there. If this happens to be the actual main kernel file for the entire system, I wonder what it's doing exposed like this. If it's a copy of the actual kernel, I wonder if it's safe to delete it without severe reprocussions. Either way, I'm not sure how to continue as long as I have it out there.

Hid the kernel file successfully.

I was considering your other advice over the last few days, when I was going through a few threads on single-user mode, since I was also considering using fsck to check the drive. I saw instead something on using Disk Utility to check the disk file structures, so I did that and then re-ran it from Recovery Mode when I was told there was an error in the multi-linked files. It turned out to be an orphaned file of some kind, so I fixed the directory structure before it could become a major problem down the road. I'm still getting the slowdown in the first three minutes of operation, though, and Calendar's Dock icon still takes its time going from July 17th to the current date. I might try Safe Mode for these issues, but I still wonder what could be causing them. Now that I've run the deirectory structures check in DU, I shouldn't need to try somthing like fsck, but it might still help.

No repeat incidents of Outlook auto-launching on startup, and I don't have the "reopen windows" option checked in the Shut Down dialog either, so that's good at least.

Quick update: Just tried Safe Mode a few minutes ago, and things were quite different. Everything loaded quickly, and Calendar's Dock icon went right to the correct date. Everything loaded except a couple of menulets, and I think one or both of the corresponding pieces of software related to them may be to blame for the slowdown.

One menulet that didn't load was for the StuffIt Deluxe Magic Menu, which has been working for me since before I upgraded to Mountain Lion, but which hasn't been updated itself lately (it's still at v15.0.4 after the better part of a year or more). Two others that didn't load belong to the Intego security software I've been using on my system for at least a year and a half. One is the NetUpdate menulet that allows access to all the installed programs I have from them, including the NetUpdate utility that updates everything; the other is a network traffic indicator that I could probably get rid of, since it just shows me upload and download rates. One of these items or programs may be to blame, although I suppose I'll have to inform their respective manufacturers about the problems I'm having with them, and ask for updates to fix those problems. At least now I know what may be causing the slowdown in the first place.

I just finished updating StuffIt Deluxe to 15.0.7, which was just released with no fanfare (I check MacUpdate and Cnet Downloads for 3rd-party updates on a regular basis, and it wasn't on either of their lists). So far, that doesn't seem to be the culprit, so I guess it's the Intego security software. Thing is, though, there's nothing in my Login Items that looks like it directly affects the core of that software, so I'm thinking it must be a kernel extension it uses. In that case, I don't think I can disable it myself without affecting all the programs connected to it, not just the security software. I use Intego's SecurityBarrier suite, which also includes system backup and program cache cleaning utilities, so disabling the extension might also affect those programs too. It's a thorny issue at the least. I may have little recourse but to complain to the manufacturer about it, as I said before that I might have to.

At the least, this might explain why I got those bad install errors I mentioned in the second item of my starting post. Interference from security software could be the reason for that.