Slow MacBook Pro. WAY too slow.

Answers regading to the numbers:

1. o.k.
2. The BOOTCAMP is needed. The second disc is maybe the device, which cause some delays. You didn't prefer to have an external disk, which can be mounted and unmounted when needed? The problem is, that during boot, the kernel will load just needed driver. It is important to have small kernel. If some special hardware is needed with drivers which are not in the kernel, a kernel-module is loaded. If kernel and kernel-modules are both from Apple, fine. If the kernel-module is a third-party module, this can be problematic. And Apple have with their own hardware-platform which they support with their drivers. More details http://en.wikipedia.org/wiki/Device_driverVendors of several disks can use the framework from Apple to develop the drivers for their own disks. Sometimes vendors just use the actual specification so drivers in the kernel will support them. But those specifications sometimes change ... I can't really allocate the problem, but in the log I can see that you OS have problems with one device. Maybe the removed optical disk, while searching it, or the new disk which is "probed" by several drivers. I suppose your second disk is with the NTFS-partition, which is mounted during boot. This means during boot tuxera must be activated, will check its license, the partitions is mounted, while MAC OS awaiting the partition to be available, for logging with fseventsd ... this cause a lot of traffic between the processes, sending requests, waiting for response and start the next process. I love processes to start when I need them, not being started because of the eventuality of their presence.
3. Automatic mounts are normally included in "Preferences", "Users & Groups", at your "Login Items". There you can remove the services which will start at boot/login time. But it's possible tuxera manage that - Sorry, I never use it. I did have a look on the /etc/fstab, which seems to be obsolete since Lion. Have a look at "Login Items".
4. Could be the I/O problem mentioned in 2.
5. I prefere to use Parallels or VirtualBox (VB belongs to ORACLE, former SUN and is OpenSource). The advantage is, I never need to change something on my system settings. The disadvantage is the less performance of Windows running in the box. If you use graphical software, like CAD porgrams, parallels will cover your needs. I use 2 CAD programs in parallels but in VB I have some problems using them. I don't use Windows for creating or editing issues, just because of compatibility reasons I keep a XP installations. Sometimes I recieve from customer data which I can't read on my MAC. Almost CAD data.

I don't know if this is a solution for you, but I would use parallels or VB. At the second disk I would use a MAC OS Extended (Journaled) partition. All the windows data I would pack on this partition with a dynamic disk size.

I use a similar configuration and I use Windows maybe one hour per month. But in the rest of the time I use MAC OS.

But notice, Windows will be less performant in the box.

Yes, if you intent to change/reinstall the OS, backup your data as Linc advice.

One, maybe noticeable thing, if one of the virtual possibilities are an alternative for you, both offer the possibility to have "exchange"-directories. Parallels even offer a coherence mode, in which the Windows programs behave like OSX apps. In this mode you can use all available directories.

1. You are right in all points.
2. Also right in all points. Of course remotely we all don't really definitely know what the source of the problem is. But you have to decide what to do and you decide. You just want to know, what would be the best way.

Ragrding to your todo's:

1. My advice is backing up data always on a external drive, now and in future. If for some reason, your system will crash, a second partition with your data doesn't help you. The backuped data, being on a external drive, you always can attach it to another MAC and read your data. It's not so fast, but much more sure - and security is the reason for making backups, not the speed.
2. Do you still have your install image ML?
   1. If not, indeed, you need to install a dvd drive (external is also possible) and install SL. After installation of SL use the migration assistant to import all your data and system configurations. Hope that works, regarding to AppStore. Because being in AppStore you can load ML again. Maybe a copy of the image would be good, so far you need one day to reinstall your OS. Do the copy, before installation process starts.
   2. The other way is of course the recovery method, which is described in http://support.apple.com/kb/HT4718?viewlocale=en_US I never did a "recover", I don't know if the installer expects a proper system. I suppose you don't need to care about that. The recover method anticipate a problem caused a system crash, which leaves some skeletons ... I think you don't need to care about the optical disk.
3. If you backuped your data on a external device, the second disk is free. Suppose the disk is included in the backup.
4. Yes, also very well described in the link above.
5. This is a very good idea, regarding to the second 1. of this message.

I found out, you can load Mountain Lion from AppStore so far you buy it.

The AppStore ask you if you still want to load it, but you can download the image. This is a very useful way to receive the image.

After backing everything up, (I know, you need an additional external disk to swap some data), partition your second disk with Extended Journaled Filesystem, GUID Partition Table - and give the partition a name.

And then start to install.

I was having basically the same problem. I had a look at my activity monitor and noticed that Photo Stream seemed to be using quite a bit of the resources. I disabled it and voila, back to lightning speed. This is just an observation and probably not a cure for a lot of these problems.