I don’t think the pushrod can be set far enough in to cause damage when refitting pressure plate, but I’d wind the adjuster on the sprocket cover back so the you can tell when you have the plate on correctly.
The movement of the pressure plate in use is very small, a couple of mm perhaps.
Are these new springs the OE Yamaha ones? Many people, myself included, have tried aftermarket heavy duty ones which are far too strong and it makes the clutch very tiring to operate.
The Yamaha springs are just strong enough to do the job, but weaken over the years. That, or the use of unsuitable engine oil, causes the clutch to slip under load.