How can I get my 3rd party SSD to boot El Capitan?
You could try using bless to verify whether the disk is recognised as bootable and to potentially bless the disk to make it bootable.

If you can boot into Single User Mode (hold down command-S while booting) or launch terminal from an installer disk you can run bless

First I would try to establish if the drive is bootable or is flagged as the boot drive all by using

bless --info /Volumes/yourSSDdrive The state of your drive's blessed system folder

bless --info The state of the current boot drive's blessed system folder

bless --getBoot The current actual logical boot volume (e.g. /dev/disk1 )

If you find your drive is not blessed, you can bless it yourself with 

bless --folder "/Volumes/yourSSDdrive/System/Library/CoreServices" --bootinfo --bootefi

See the man page for more details:
https://developer.apple.com/library/mac/documentation/Darwin/Reference/ManPages/man8/bless.8.html