Yosemite on SSD boots from USB but not when the SSD is installed internally
Just because the hardware is set to remember where the last boot was from and will look back to it at the bext boot, I can recommend you to hold down the C button right after you start up the fully assembled system and then select the SSD again. 

Also note that the cable that connects the internally placed SSD may be damaged/disconnected somehow or even the Motherboard could have a problematic/defected chip.