1) How hilly is the ride from Myślenice -> Zakopane and for what portion (ie just the last 10kms or the entire 60kms)
It is mountainous, the difficulty with answering a question like that is, I don't know what you are used to.
Myslenice is in the Beskid mountains, they are great for cycling and the closer you get to the Tatras the more mountainous it becomes.
I will put it another way, you'll be able to cycle it, it is very beautiful too.
2) What sort of weather can I expect? Obviously if it was still snowing I would have to call it off, but the last time I was in Krakow in April the weather was gorgeous, just wondering if that was an exception to the rule, or April is usually nice?
yes, it'll be good for cycling, as mid summer is too hot for comfort.
I would recommend cycling to Myslenice and going on one of the many bike routes through the forest and over the mountains to Zakopane.
There are trekking huts where you can stay the night along the way.
The motorway would not be as nice as going through the mountains but I would give myself 3 days for that.
Let me know if there is any further information you would like.