OP here. I ended up replacing the front pair as well. It is possible to DIY but you'll need lots of patience. The strut goes into a tight sleeve at the front-wheel knuckle, which is held on by two bolts. It is a PITA to put the strut back into the knuckle sleeve. I had to repeatedly raise and...
I'm an Si owner thinking about switch to an MS3 as well. What are your thoughts on the MS3's clutch? Lots of reviews have complained about the MS3's clutch engagement.
If you like the stock ride, KYB shocks and struts will do the trick. There's no need to replace the springs. I got my front and rear KYB's from Amazon merchants. The front struts are a pain to replace. You'll need a spring compressor tool.
I'm not sure what a "side cup holder" is. The easiest way to remove the top nut is with something that can hold the flat faces of the rod stationary (like a vice).
IMO, you do not need an alignment after replacing just the shocks. The suspension geometry stays the same with the stock springs.
My '06 Sport didn't have an alarm. I have the immobilizer, a panic button on the remote, and a blinking light on the dash that pretended I had an alarm.
The clips holding the plastic door panel are pretty sturdy. Just make sure you don't apply any lateral force, pull straight back. Don't be afraid to yank.
I'm pretty sure your lock actuator has failed. This has been a common problem with the Mazda5. Just do a search here.
I have done the replacement myself and posted a DIY for the replacement:
http://www.mazdas247.com/forum/showthread.php?123761729-Sliding-Door-Lock-Actuator-Replacement
I just updated my original post so the images would be displayed inline with text. How come the How-To forum can't display multiple pages? It seems that these DIY posts disappear after a while.