Sorry, I have no experience with HDDFanControl. I've been using smcFanControl -- but not for this issue -- without any harmful effects. HDDFan is new to me, but I don't see how it could be harmful. I guess I'd just want to be careful not to configure it to run the HD fan too much above the defaults, as you don't want to burn up the fan motor. Get iStat Pro so you can keep an eye on temperature and fan speeds.
http://www.islayer.com/apps/istatpro/
Although it won't show the fan speeds, Temperature Monitor is noted for accuracy.
http://www.bresink.com/osx/TemperatureMonitor.html
As for using the enclosed cables, I guess you'd just have to try and see what happens. If you think you can open it up again without any unnecessary risk, if it works, this would seem to be the preferred solution. If it doesn't, I guess you just leave it like that and continue to run HDDFan.
Perhaps you want to contact Seagate at 1-800-SEAGATE. Ask for Pre-Sales, since they will be more knowledgeable than the outsourced, mediocre Level 1 techs who, at best, will probably just be reading from a script.
For the cables, you could also call OWC tech support, 1-800-275-4576. And also ask them about HDDFan, since they have been recommending it for the 2011 iMac drive problem.