Slow down on this one... Before you slice up a battery, try this... On my ego kit, I find that sometimes, to your point, the hole doesn't line up with a slot in the battery, BUT there are two spots threading can start if you know what I mean. I find that if I loosen the sapphire while keeping pressed to the battery until it skips to the next thread, then tighten from that point, the hole lines right up.. Hope this makes sense.
I've also experienced the heat issue, and it seems to be due to wicking issues and the coil getting too dry. I find popping the fill plug sometimes releases some air and lets more juice back in.
Haven't had any leaks on the sapphire yet, but I've also had some other setups get hot when theres a bad connection to the batt due to juice in there. Just something worth checking if you think the coil is wet enough.
Hope this helps!!
