Each power connector has a max power that it is expected to deliver, as long as you arent using splitters or adapters to get additional connectors off of a string you can use all of the connectors on it without needing to worry.
They wouldnt have put 3 SATA power connectors on the string if it couldnt power all of them safely, same with the PCI-E connectors.
Would it be ok to use an male to female 10 inch extension on the hard drives.(not a y connector) for the two of the hard drives. See link below - the top item on the page.
(((8 Inch Long SATA 15-Pin Male to Female Power Extension Cable 15-F to 15-M))) http://www.satacables.com/index2.html
The main reason for tha tis my power cables are so stiff, and I don't have alot of room.