Best way to hook up eight 12 volt batteries for 48 volt system...

At the risk of being overly repetitive:
If you are concerned about resistance/conductivity, go basic. Measure the voltage drop and current draw on each cable segment with the largest load that you can muster. Isn't that the whole point?

Dynamic testing with a load, using a DVM set to milli voltage scale, lug terminal, would reveal if there is a volt drop, volt drop would  mean resistance. As @bill von novak stated contact resistance renders them unsuitable for trouble shooting, the ohms per volt of the meter is also a consideration, when tracing ground faults on fire alarm systems, I would use an analog meter as the DVM would read all over the map, insulation testers are useful for that purpose too, with extreme caution.

softdown said:

Still might be useful for finding a bad connection with the lugs?

Generally not; it's hard to detect a .1 ohm difference with a meter, even though a .1 ohm increase will result in 250 watts of heat in the connection if you are drawing 50 amps.  (And 250 watts will quickly make the problem worse.)

If you really need to measure resistances down that low, then get a 4-wire meter.  They are much more accurate.  You can also use two cheapo meters and a lab supply to do the same thing - send 1 amp through the wire via the lab supply and one meter, then use the other meter to measure millivolts on the WIRE ITSELF (i.e. lab supply and second meter connect to different points.)  Then it becomes easy - 1 millivolt on the second meter is 1 milliohm of resistance.