When i finish nidoranM manip i start biking down, and in the notes it say that the menu will pop and i have to fly to pewter. I have tried opening the menu manually but i dont get a scyther. Thanks in advance.

The most likely problems are:

1. During the PC underflow section, you may not have counted slots correctly
2. At the beginning of the safari zone, you may have messed up the Pokeball swap
3. You may not have biked down far enough

1 is almost certainly the problem though.

Thanks, i will try it again