It seems to me that you should use a TR of 4 seconds,
but when you run to3d, you will have to use the '@filename'
technique for specifying the slice timing (since it does not
divide the TR regularly).

If you do not use to3d directly, that is okay. When you are
going to use 3dTshift on the data (before registration), use
the '-tpattern @timing_filename' option there, instead.

A tpattern file for 10 slices captured in 3 seconds (in the
alt+z format) might look like:

0 1500 300 1800 600 2100 900 2400 1200 2700

Those are ms offsets from the first slice, alternating in the
z-direction, lasting 3 seconds (even though your TR is 4s).

- rick