Not sure why you would swap out the dielectric nipples - corrosion over the long haul? I see Tom Lane reccommends against ANY galv fittings, and I guess those dielectric nipps are galvanized...I definately would use tape & dope on the brass nipple threads, IF you're NOT using glycol. If you ARE using glycol, then just use teflon tape. Try to use RED brass nipples as opposed to yellow brass nipples (less zinc). I suppose you just need some oomph to remove the dielectric nipps. Try a larger monkey wrench & pipe extension handle w/ someone to bearhug the tank to keep it from spinnin'.
Regarding the correct ports to use, this tank has no internal heat exchange coil, if I'm not mistaken. You didn't mention whether your existing solar system is pressurized glycol or water drainback - if you're glycol, then you can't plumb direct without interfacing a heat exchanger between the domestic water supply and your glycol filled collectors. Yes, heated fluid from the solar collector goes into the tank up high - make sure there's no long dip tube to the bottom in this port. You are correct to use the lowest port available for the supply to the collector - the collector wants the lowests temperature water that you can give it for maximum efficiency. Best of luck!