Chain crunching after degrease and lubrication I did the usual degrease and lubrication on my mountain bike today but when I tried to ride the bike later on I heard pretty bad crunching sounds.

The sound is definitely coming from somewhere around the drivetrain and becomes more prominent with a more forceful pedal. I can only reproduce the sound when shifting to the middle cog using the front derailleur. The sound is not made on the small cog on the front but is still made slightly on the largest cog using the front derailleur. The sound is worse when shifting to the smaller cogs using the rear derailleur.

The bike is also now struggling to shift to the highest cog using the front derailleur from the middle, it looks like the front derailleur may be misaligned somehow during the process, this was not the case before I cleaned the bike, does this sound like a possibility?

I also opted for a more thorough clean of my drivetrain this time round and removed my entire back wheel, could putting the back wheel on incorrectly have caused this problem? Alternatively, could this also be a sign of chain wear?

I have only clocked around 200km on the bike so far. The bike is a Calibre Two-Two with Shimano derailleurs and gears.

If any additional details or photos are needed, please ask and I will provide them.
If the sound started suddenly after you cleaned the drivetrain very likely something got misadjusted or knocked out of alignment. Any issues with chain wear would show up gradually, also 200k is nowhere near enough mileage to put significant wear on the drivetrain. 

Issues with changing chainrings indicates the front derailleur got knocked out of alignment. That's easy to do accidentally. It's likely you are getting some bad chain-rub on the front derailleur cage If you can hold the bike of the ground, on a work-stand for instance, manually turn the cranks and work the shifters you should be able to figure out if the sound is coming from the front or rear derailleur area.

If you have a through axle rear hub you can't misalign the wheel in the frame. If you have a quick release hub it's definitely possible to not get it in the dropouts properly, so check that. Stand the bike up vertically, loosen the quick release, make sure the axle is seated in both dropouts and tighten the release again.  

I'd run through a complete front derailleur adjustment process to get rid of the chain-rub and make sure the adjustment is correct. Park Tool has a great page with videos that includes triple chainring derailleur adjustment. Thay have a rear derailleur page as well if you feel the rear derailleur needs a tune up also.