Okay, I'll answer my own question, but if anyone disagrees with me, please let me know!
Every parts site that I searched seems to indicate that the struts and springs are compatible across all years/models of the 986 Boxster. Not compatible would be parts suspension from a 987.
The springs/struts I'm getting were pulled of a 2003 Boxster S with approximately 3500 miles. They were replaced with aftermarket parts. The OEM springs and struts went into a box and have been in garaged storage ever since.
I'm replacing all the suspension components, front and rear, (control arms, tie rods, drop links, sway bar bushings, etc) at the same time. Should ride like a completely different car.