i'm not sure what you are talking about? grinding out the cases to match the kit or grinding the kit transfers to match the cases?
either way it probably wont make any difference on that setup, my guess would be that you need taller gearing. Thats gonna make your first gear clutch perform even worse, but thats just the way it goes. That is a super low rpm kit so its not gonna work well with that clutch which is designed for a kit making more power at high revs. They do respond well to porting, so if it were me and i were searching for that elusive 55 mph number, i'd hog out the exhaust port and upgrade to a VM22
if your port timing is wrong and you need to shim the cylinder up, that will kill your top end as well, but to be honest 45 is probably about right for one of those, they just don't make a lot of high rpm power... they are nice and reliable and make good torque with the estoril so maybe the easiest thing to adjust would be your expectations.