Okay the reason the lowered mounts are needed is because you are putting a plate on top of where the mounts bolt to the hull , I believe they are using 3/16 plate so when you bolt everything up the rear mounts just have holes the stock bolts go through then the mount sits on top of the plate , on the front mounts those are extended forward and the plates are drilled and tapped for the front mounts, the old front mount location also have just holes and the plates bolt to the old locations, its the same thing I did on my 300SX conversion basically .
Long story short , you are raising the mounts up 3/16"higher with the plates so the mounts need to be 3/16 shorter than the stock mounts to compensate .
The other way to do it is the link below , using the ADA adaptors, these of course use stock mounts.
https://www.adaracing.com/yamaha-engine-mount-conversion-3-cyl-blaster