The clutch pads would not cause things to go slow, but not function at all. If they have glazed over they could slip and not grab well. Causing you to go slow but you would feel them just slipping.
The spring on the clutches can have an affect on quickness but not really top speeds. If you have a stock spring on your second gear still then it will spin and engage early before you have a chance to get into the powerband. This will cause the bike to slow and bog a bit but ideally it should slowly get back up to speed.
Again this would not be limiting any top speeds.
Tomos stock cdi and points both seem to cut out around 9k to 10.5k RPMs no one on here has ever given a great answer to why that is, but it always seems to be a thing. But that again you can feel this while riding. It will feel like the bike is still gaining speed at the top, then all of a sudden just kind of hits a wall and won't go past that rpm even tho the bike feels like it should. Then it almost starts lurching from trying to go a little faster but then gets "limited" back down a bit. It is kind of weird and entirely frustrating.