G'day mate, by the sound of the engine bogging it sounds like you have not yet tuned it correctly to suit the air filter. I don't have a four stroke scoot myself but, other members had fitted free flow filters and upjetted to suit, but I think the exhaust was too restrictive, some had a restricter washer inside the exhaust. If the exhaust can't handle the extra flow after changing the filter, I think some people were drilling holes in the exhaust. The better option would be to buy an after market exhaust, but it is all money. Try tuning your carb and see how you go with that, it is repetetive and time consuming, but if you run the engine too lean you can do serious damage to it. If you put in a larger jet, take it for a ride and see what difference it makes, if worse try a smaller jet, if better then you know you are going the right way. Do a search on the forum for plug chops, there are explanations on the subject that are better than I can give. With regards to the rattle, first look at your variator, if the slide bushes are worn or missing, they will rattle. I replaced my variator last night, my last one rattled like it was about to drop the crankshaft. Also check your valve clearances are to spec, another source for rattles.
Stick with it and you will have a lot of fun, though they can test your patience at times