Oh yeah,a socket and hammer most likely didn't do it any good.I'm not sure if Yamaha sells the bushing install slugs or not,I doubt they'd call them a slug anyway,but I had a machinist friend of mine make me a couple of different ones.I have one for the secondary and it'll do the helix and the sliding sheave,both the same bushing,plus he made me one to do the sliding sheave of the primary.What the slug does is it has a shoulder machined the exact OD of the bushing with an extension that fits the ID of the bushing,that way when you press it in it won't crush the shoulder of the bushing,which I'm afraid you might have done.
If you can't find any place that sells the correct slugs then your only recourse would be to take the bushings to a machine shop and have some made.I'd definitely advise having one made to do the small one that goes in the outer primary cover,I've managed to mess up a couple of brand new ones so far by using a socket and a vise to press it in.Unfortunately my bud doesn't work at the place he was at and I didn't get one made but it's on my list of things to get done.