Sometimes install order matters. I'll go through the order I'm doing things, just so you know. If you did things in a different order, let me know.
Ran MCPatcher first, because I don't actually know what it changes, and I don't want it overwriting ModLoader files. Installed ModLoader. MCPatcher removed the META-INF folder for me.
Minecraft loads fine. Load into a single player world just fine.
Installed GuiAPI. Loads into game and world just fine. Good to know all your utility mods play well together.
I'd install ID Resolver now, but it doesn't look like you're actually using enough mods to need it, so I'm not sure where your ID conflict came from, but we'll see. AutoSwitch next (I always wonder why they bother putting mods with only one file into a zip folder.) and it loads fine.
Timber mod looks like it works just like Treecapitator.
Installed that next. Ok, possible issue here. The website you linked says to install the mod into the .jar file, but the readme in the actual file says not to. Obviously, if you installed this to the jar, it could cause problems. Also changed the AutoSwitch config file to IGNORE=false. Made a shovel and an axe to test AutoSwitch and Timber. Timber seems to work just fine, but AutoSwitch doesn't seem to be working. AHA. The config file has AutoSwitch disabled by default farther down. Hm. Still have to toggle it on with F10 before it works, but it does work.
Installed InvTweaks into the mods folder. Inventory sorting works, stack swapping doesn't seem to. I chopped enough trees to break my wood axe, and it didn't move my other axe into the hotbar. I then started experiencing severe lag issues. Reloading into the map didn't help, and I crashed out with a memory error. >.< If you have that problem, I suggest installing Optifine. Fixes it for me on my other Minecraft installs.
Restarted the map, and no more lag. Just too many saplings floating around, it looks like. Turned off AutoSwitch to wear out another axe on some dirt (since there's no longer any trees nearby) and InvTweaks replaced the axe when it broke. Item stacks are also being automatically replaced, so it's working.
Installed MineColony. Starts up just fine, and I can craft the Town Hall chest.
I didn't install IDResolver because I didn't experience any errors that made me think it's actually necessary.
So it's looking like an install error. I don't know where the wiki says that the 105 slot error is due to putting the properties file in the wrong place, but it does sound plausible that that's the problem, since you tried to change block IDs and that didn't solve the problem.
So definitely try installing the mods manually. ModLoader, GuiAPI, and AutoSwitch go into the .jar file. The rest DO NOT go into the jar. If you *really* want to, you can use MCPatcher to install ModLoader, GuiAPI, and AutoSwitch, but using MCPatcher to install the other mods will cause errors. You'll have to use the F10 toggle to turn on AutoSwitch, and you may have to edit the config file (located in your .minecraft/mods folder) but the mod's thread says it should work if you don't, you just can't change hotkey buttons and such.
The zip INSIDE the Timber! zip you downloaded goes into the .minecraft/mods folder, as does the actual InvTweaks zip file you downloaded. Minecolony has several folders that need to be in the mods folder: MineColony rc17.zip, gui, minecolony, mob. The floorplans file must be in the .minecraft/resources folder, and the MineColony.properties file must be in the .minecraft folder. Check to make sure the files and folders are in the correct place. If they're not, you'll obviously have to re-install with a fresh minecraft.jar. If they are, you still may wish to try to reinstall.
Let us know if you still have problems.