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I'd really suggest reading something like Andy Sperandeo's book from Kalmbach, "Easy Model Railroad Wiring." He has a lot of good advice for reliable wiring, and it will cost you less than one RTR freight car.
The book is out of print at Kalmbach but available online and at shops and swap meets.
Yes. The joints are always a weak connection point, if not when the rails are installed then it will be someday. Another problem for me has been in the turnouts. I have to jump across turnouts from time to time, so now I just jumper them all.