It's not impossible and completely in the realm of a small engine mechanic/decent auto mechanic's skill sets.
There are a few special tools required to get the engine apart in addition to basic hand tools (wrenches, sockets, hammers, etc)
First, you need a flywheel puller to fit a blaster ($15). You need a case splitter ($59 for the tusk model) and a crank puller ($59 for the tusk model).
You also need an impact screwdriver ($10 for a cheapy, more for a good one) and some external snap ring pliers ($10 for a cheapy set, more for good ones)
I recommend a flywheel holder/clutch holder ($25 or so) but you could make your own versions of those from scratch if you had some time.
You start by draining the transmission fluid and removing the carb, pipe, spark plug wire, oil injection lines if still equipped, chain, swingarm pivot bolt, and two motor mount bolts. The engine should be able lift up and swing out to one side (I prefer left side, only because the kicker makes a REALLY good handle for the right side as the engine is coming out)
Clean off the work bench and remove everything under the clutch cover and the stator cover. Also remove the entire top end.
Remove the 10 case screws using the impact screwdriver and lay the bottom end on the left side (stator side). Using a rubber mallet, tap the right side case upwards checking to make sure it's coming off smooth. If it doesn't come off smooth, STOP and recheck that everything's off like it's supposed to be.... It should be come on up with minimal tapping (to free the sealant and alignment dowel pins).
Once the right case is off, remove the transmission components from the left side case and use the case splitter to push the stock crank out of the left side case.
You need to slide the two cases together (empty) and check for case misalignment at the "inlet" and "outlet" of the cases. The +3 vito's crank doesn't need trenching but occasionally the very front and back of the crankcases need filing. Now pull the cases back apart and slide the crank into both sides as far as it'll go (separately of course!). The crank should slide into the right side case and you can check that side easily. You shouldn't HAVE to pull it into the left side case but that is the "thrust" side bearing so it won't slide in easily....
Usually one or the other is too far in and will hit the big end bearing when the crank turns. If it needs filing, make sure to do it before installing new crank bearings
Replace crank bearings as needed (and budget allows). If you're putting new crank seals in (which I DO recommend) you can install the right side now, but wait for the left side.
Coat the crankshaft bearings, main bearings, and wrist pin bearing in 2 stroke oil now, before you forget...
Pull the crank into the left side case (MAKING SURE THAT THE ROD IS HANGING OUT OF THE CYLINDER OPENING!!!!!!) and resinstall the transmission into the left side case as well. Align the shift star and coat the right side case with sealant. Install the right side case "down" onto the left side case and install all of the case bolts (don't forget the stator bolts, you don't want sealant curing in those threads). If you did buy new crank seals, now is the time to coat the left side seal with 2 stroke oil and drive it into place using a seal driver (or a large deep well socket if you don't have a deep seal driver). Make sure to drive both crank seals ONLY until the seal bodies are flush with the case bosses (the highest point of aluminum surrounding the seals)
Once the cases are together, turn the input shaft (the one the clutch goes on) slowly and rotate the shift drum to make SURE you have all six gears with neutral between 1st and 2nd. Do this NOW so if you didn't do something right with a shift drum you'll know it now instead of later when you try to ride the quad.
Go ahead and install the piston (using new circlips!) and install the top end on the bottom end.
Once the engine core is reassembled (but obviously before the clutch side is reassembled), use a leakdown tester to test for leaks. The LAST thing you want is a brand new engine ruined because of an airleak. It's easier to fix any airleaks you might have now, before the clutch side is all reassembled.
Follow the service manual to reinstall the clutch cover components and stator cover components taking extra care to properly adjust the clutch engagement.
Pour a liberal amount of 2 stroke oil down into the intake manifold just to make sure you've got enough floating around in there and put the engine back into the frame.
When you start it up, you need to treat it as a new engine, break it in by letting it idle for 3-10 minute periods and recheck the base nut torque and head nut torque.
Once you've got it retorqued, tear out!