Below are some of the more successful modifications I've made that conflict with the plans. I wouldn't recommend that you make any changes to the plans unless you are absolutely sure you fully understand the consequences.
Quite a few of these suggestions are design compromises - in other words the craft/plan designer has selected a particular design feature based on different criteria to the criteria I'm using. In other words, the plans are not wrong - they are just a different design compromise.
One significant change I've made is to double over the skirt at the inner skid attach points. This is done to make the inner attach strip stronger than the outer - that way if the skirt snags the outer will give way before the inner. You can't easily get to the inner strip on a large craft on a trip to make a repair so I'd rather the outer gave way first. One other thing worth doing when assembling the skirt to the craft is to melt any bolt holes needed using a soldering iron rather than punching the hole. Melting seals the internal mesh and makes the hole much less of a weak sport in the skirt.
Another modification on the larger craft is to beef up the front quarter inner attach points. A strip is normally screwed into hard points on the underside of the hull using self- tapping screws. I've found that this is inadequate when operating on rough water - the front compartment gets severely pressurised when you drop into big wave troughs and has pulled these strips loose a few times. My preferred method is to bolt through the hull using 4-5mm bolts and nuts.
The other weak point on the Prospector skirt is where the rear skirt inner attaches to the lower edge of the vertical duct. This edge (which has a small upward sloping edge) is very exposed and the strip and screw heads get whacked when operating at low hover height over rocky or pebbly beaches. Eventually, the strip and screws let go resulting in skirt tears in a very awkward place. After repairing this area several times I fitted a small metal plate strip bent to form partway up the inner edge of the duct. I also used countersunk stainless screws. This stiffens the edge and provides a smoother transition. If building again I would probably add a central V section horizontal stiffener over the duct hole and extend the centre skid backwards to protect the skirt attach edge.
Firstly, remove the fuel cutoff solenoid from the bottom of the carb float bowl. This solenoid is a well known source of problems on these engines - it gets jammed easily by debris in the bottom of the float chamber and, if it fails, will disable the engine immediately. Replace it with the correct thread bolt - make sure it is sealed and doesn't protrude too far into the float chamber. The solenoid prevents unburnt fuel being sucked into the engine during shut off (the ignition is switched off so the fuel isn't burnt). To minimise this problem you should remove the governor and connect the throttle cable directly to the carb butterfly valve. The other advantage of doing this is you are removing all of the delicate governor mechanism (springs, thin plate levers, etc) and their potential for failure at the wrong time!
The other thing I would do is to lacquer or paint the uncoated external surfaces of the engine. The flywheel is typically unpainted cast steel. The aluminium engine block is also usually untreated (and will corrode in salt water!).
Also protect the coils and ignitions leads. The coils should be carefully cleaned then varnished or painted to seal the iron core edges and then coated with silicon sealant. The plug boots should be sealed by expanding the boot where is joins the wire and pumping silicon into the gap. Don't worry about how neat it looks - its more important that it is waterproof!
Prop pulley bearings and mount
Place the top pulley between two pillow block bearings rather than having a long overhanging shaft as per plan. To do this you need to modify the top part of the engine frame to add a rear overhanging support frame (and remove the front overhanging frame). The downside of this mod is that it makes it slightly harder to remove the belt - in reality, it's quite a job anyhow as you need to remove both fan belts and the rear engine support bar. You will also need a to use a prop hub rather than the torque tube arrangement defined in the plans (it's probably easier to make a hub using a small cast pulley (see above).
Make the idler pulleys fixed rather than adjustable and use a pivoting mechanism on the top pulley bearings to move the prop shaft up and down to tension the belt. The main reason for doing this is to that the alignment of the belt to both drive and prop pulleys will remain virtually constant rather than changing as you re-position the idlers. The second reason is that you would need very little adjustment range at the top pulley - you are adjusting both sides of the belt at the same time - about 20mm would be enough to let you get the belt on and off the pulley. The top adjuster would be less complex than the idler swinging bracket arrangement described in the plans (look a the top adjuster system used on the Prospector and Explorer).
Vertical shaft engine fan hubs
On the smaller Sev craft that have single vertical shaft engines, the fan is bolted directly to the prop driver pulley using spacers and bolts. This setup is very difficult to assemble and disassemble. It's far simpler to use a small separate hub for the fan. The hub can be made by buying a small diameter standard belt pulley (smallest belt size you can find) with a flush taper lock then drilling and tapping three or four M8/10 holes into the flat outer surface to attach the fan using bolts. The fan should be centre drilled to locate on the engine shaft. You should also use a long key that passes through both the prop driver pulley, the fan pulley and the fan itself. You can machine off the fan pulley belt groove to save some weight. The disadvantage of this mod is slightly more weight. The advantage is ease of assembly, lower load on the prop pulley and simple drive belt removal by unbolting the fan from the hub.
Sevtec craft all have flotation compartments designed to support the craft when stopped on water. They work just fine but if they are punctured they can severely reduce the flotation capacity. The solution is simple - fill them with lightweight empty plastic bottles (milk cartons, inflated large bubble packing, etc..). There always seems to be a small amount of water in these compartments - I think this is probably due to condensation - it's easily to remove using a sponge. If you need to check whether a compartment has any leaks then just fill it with water and look for any escaping (make sure you support the underneath of the hull - water is heavy). You shouldn't need to fill it full - any leaks will almost certainly be in the lower half, near to the ground.
On the smaller Sevs where there are two flotation compartments I would add a third or fourth just by sub-dividing the existing ones front to back. This will significantly reduce the effect of a hole in one of them.