318/360 heads,with thumper cam

To answer your question, yes a slight rocking would be normal. It's just the piston to wall clearence.

Now to the big picture. From the info. you have provided you've got some clearence issues that are only going to compound themselves with the modifications your talking about doing. Head milling, zero decking and possible piston replacement are going to require checking valve lift, pushrod length and intake manifold fitment (milling) and so on.

At this point the only thing i can recommend is find a good reputable machine shop and let them evaluate what you have and what you need. For a durable, good running engine, all these thing have to work together. Just piecing it together is not going to get you where you want to be. It will cost a little more and take more time, but in the end i think you'll be much happier with the results.