This is an interesting idea...How fast is the acquisition time of one of these readers if the shoe passed over the reader quickly?
You'd have to ask the manufacturer or supplier. I've no idea.
Could I make the reader "long" somehow? That is to say, more like a pill shape vs. spherical? Or would I need a couple readers next to each other to cover a 3 foot wide path?
Place your feet together and measure the width of both feet. Mine are about 9 inches. If the reader is in the middle of the path then the nearest foot would be about 9 inches away. Most people don't walk or run with their feet close together or wide apart so I guess your 'acquisition' area would be in the range 0 to 10 inches.
To reduce this, you could narrow the path at this point with (temporary?) obstacles to form a chicane, or build a kissing gate http://en.wikipedia.org/wiki/Kissing_gate
with the reader in the 'D'.
As you haven't said where this will be deployed (public or private land), it's hard to give you a definitive answer.
You'll need to protect the reader from damage from being stood on, so I suggest covering it with a hard plastic sheet. You'll also need to ensure that it isn't a trip hazard.
I know little about RFID, so all I'm doing is suggesting alternative methods of placing the devices. You'll have to check that they are practicable.