Here are some things I've learned while building hovercraft - a lot of them have been learned the hard way
Use cast (or better still, plastic) pillow blocks rather than the pressed steel type specified in the plans. The extra weight (zero in the case of plastic) is insignificant and is worth the added strength and rust resistance.
Buy good quality double or triple seal bearings. The bearings in a hovercraft are difficult to keep water and grit free. If using plastic pillow blocks then fit the optional end caps (filled with grease). If not, make up a thrower (a simple plastic disc at least the same diameter as the bearing) and fit it to the rotating shaft a few mm upwind of any exposed bearing. Alternatively make lightweight covers over the bearings.
Be careful not to over grease bearings - if you pump grease until it starts to come out you will damage the rubber seals. Most bearings only need to be 30-40% full internally!
Taper Lock bushes
When using taper locks the taper section of the pulley or hub and the lock itself must be scrupulously clean if you want it to grip properly. Do not grease these parts or the shaft to try to prevent corrosion (grease does not compress and will result in a loose connection once it is squeezed out of the compression joint). You can use light oil or WD40 if you must but remember that taper locks rely on friction to work!.
Keyways in shafts
Personally, I avoid using keyed shafts if at all possible. In all of my three craft there is only one key used (unavoidable on a lawn mower engine crankshaft). Why do I dislike them? Simple - key slots weaken shafts. If you do the engineering you will find that a shaft of a diameter equal to the keyed shaft diameter minus the slot depth is just as strong as the larger diameter slotted shaft. Keys have to be the correct size or they will not work properly - in particular the incorrect key height is well known to cause fatigue crack failures in taper locks. Standard taper locks, when fitted properly, will withstand more than enough torque. If you want a hi torque solution then use Tollok bushes.
If you intend to use your craft on salt water or in wet weather then I would recommend that you fit an engine cover - especially if you are using a car engine. The cover will keep water and most of the dust, sand, etc out of the engine. The cover should be designed to allow free airflow around the engine block - the best way to do this is to make the cover over the top and sides but leave it open at the bottom. With a vertical shaft air cooled lawn tractor engine it's a good idea to make the air change direction before entering the cooling intake on top of the engine. If you make the air take a vertical path then virtually all of the large particles and water droplets will fall out of the airstream before they get into the engine.
Engines fitted to a hovercraft must have proper air cleaners fitted. Unfortunately, most car and lawnmower air filters are paper cartridge based and, when wet, don't work too well. In a hovercraft there is a good chance they are going to get wet at some point! The solution is to take the intake air from someplace dry. The best place I've found is from under a seat at just above floor level (not at floor level as it can suck debris and grit). Another other good place to get clean air from is the battery or fuel tank compartment - a side effect of using these places is that the engine automatically consumes any fumes from the battery or tank vent. You can pipe the air intake using 75-100mm plastic waste or drain pipe - if you use flexible pipe make sure it's strong enough not to collapse under vacuum (engines suck a LOT of air!). Make sure there are enough vent holes under the seat to let fresh air in. If possible, make a vertical run in the feed pipe someplace to drop out any heavy particles or water droplets (make sure the start of the pipe has a downward slope to allow the water to escape). I also fit an open mesh filter to the under seat end to prevent bulky stuff getting sucked up the pipe and blocking it (paper towels, leaves, clothing, etc) - a loosely crumpled section of 1/2" mesh stuffed into the end of the pipe does the job nicely.
There are two parts to the electrical system on most engines, the HT (the high voltage spark plug circuit) and the 12V side.
The HT side should be well protected. Use good quality HT leads and, if possible, motor cycle style spark plug boots which cover almost all of the spark plug. Seal the joints between the cable and the protective boots at the spark plug and distributor/coil ends using silicon or soft acrylic sealant. Protect the distributor from water spray or vapour but make sure there is plenty of air flow around it to keep it dry (and don't block the distributor cap vent hole!). The coil should be placed in an open bottomed box or cover - make sure there is airflow around and into the cover to remove any moisture or condensation.
The 12V circuits are almost as important on a modern engine - a single bad connection or faulty wire can stop the engine running instantly. Take great care when routing wires to make sure they can't be damaged by anything they pass by. All wiring should be double insulated - in other words wrap all wiring bundles using wire tubing or tape. Make sure wires don't lie on top of hot engine parts or are subject to vibration from any mechanical components. Support wires properly when the pass over large gaps. You can buy proper wire routing parts (stand off clips, foam rub pads, wrapping tube, etc) to use for this. If you want an example of the kinds of things that are done then just open the bonnet of your car - you will see the extreme measures taken to protect the wiring harness. The result is that car wiring systems, despite being very complex, are extremely reliable.
Connectors should be positioned in "sheltered" locations where possible. They should be tied to some stationary object to prevent the movement of the connector breaking wires. Most car-type connectors, in spite of not being waterproof, will work just fine if they are located with care. They will, however, eventually corrode in salt water use. I have had mixed results in my attempts to seal or use sealed connectors. Unless the connector is 100% waterproof then moisture that gets into the connector can't get back out again quickly enough and results in corrosion. Even sealed connectors suffer from temperature cycliing condensation. I am of the opinion that they should be left as open as possible so that they drain and dry quickly if they do get wet - they should be sited to keep them as dry as possible. To prevent creeping galvanic wire corrosion after salt water use (the battery effect), disconnect the main battery (turn of the isolator) when the craft is not in use.
Both HT and 12V connectors should be positioned such that water cannot run down a wire and into a connector. It is good practice the make a "U" loop in the wire before entering a connector to allow water to drip off the bottom of the "U" instead of getting into the connector. Sometimes this isn't possible so I use a cable tie just above the connector (and leave the cable tie pull tab unclipped) to collect any water from the wiring and divert it away from the connector.
Make sure the drain and vent holes in the alternator and starter motor cases are kept clear.
A lot of this stuff may seem extremely fussy but remember that the overwhelming majority of hovercraft breakdowns are caused by, largely avoidable, electrical faults!!