I have professionally-installed Line-X in mine for the last 14 months with the UV-resistant upgrade. Came with a lifetime warranty, and I got it installed for $575 (it was $200 off as a car show special). Great product. I've tossed/shoved/dragged a lot of big/heavy/bulky items across it, and it's hardly scratched. Color is still dark black, and I don't have a tonneau or anything over it.
Iron Cross HD Step review: http://ramforumz.com/showthread.php?p=556522#post556522
Just had my Bedtred Installed yesterday for $480 tax included. It won't get your truck bed waterproof but I will save it from dents and scratches from what it seemed.
For alarm, got the stock one but am adding a remote start. Had ordered Xpresskit DB-All so I won't need another key for by just using the OEM. Paid $65 for the module and $25 for the T-harness plug and play.
I don't have a sprayed in liner in mine but my brother inlaw has had full metal jacket,and line-x in his trucks and he prefered line-x.....As far as a remote start goes I've had a python in my civic for 9 years without any issues....