In my experiences there will always be differences when upgrading clubs.. at first they're (the differences) quite subtle until you get a feel for the clubs. Every time that i've bought new irons i shoot worse for the first few (4-6) rounds. All clubs have different specs.. and you just have to feel them out.
I tried the r9 as a pro and discovered that I most definitely prefer irons with higher trajectory.. like the g10, g15, or i15. I'm currently using the g10 master set and just beginning to get the hang of it. Haven't been a master for long.
To answer your question more directly (and my disclaimer is that my experience on here is limited but these are my current perceptions.)
1. The clubs greatly affect the trajectory.
2. The spin of the ball, from what i've experienced and gathered is more of a combination between upgraded high spin clubs and high spin balls. I'm sure there's a difference even with the free balls but I think it's too subtle to notice.
3. In this game ball feel translates to swing meter speed.. and no Master club will help you with that.. only the GI2/GI series balls.