Lots of good information above. As dry as they can be, I recommend reading through some manuals, though they have some conflicting information.
PLC-5 Enhanced manual: 1785-um012 Chapter 9.
1756-DHRIO manual: 1756-um514
DH / DH+ /DH II/ DH-485 Cable installation manual 1770-um022
To answer your immediate question, no the node numbers don't have to line up with where they physically are in the network. Just no duplicate node numbers.
Basics:
-Use Belden 9463 Blue hose cable
-The signal is sent between the blue and clear wires. The shield is there to shield against noise.
-With DH+, convention calls for clear on terminal 1, and Blue on terminal 2. RIO is blue on terminal 1, clear on terminal 2. Electrically it doesn't matter as long as all nodes are the same.
Network wiring should be one of two formats:
Dropline-trunkline: No more than 3 cables leaving station connector. Two trunklines to the next SC boxes, one dropline to the PLC node. At each end of the network there should be one trunkline coming in, one termination resistor, and one dropline.
Daisy chain: RIO is commonly wired like this, though it is a legal configuration for DH+. Connections should have either have two blue hose connections, or one blue hose and a termination resistor.
Runs should be a minimum of 10 ft, with droplines no more than 100ft. The standard says not to mix dropline-trunkline, and daisy-chain, but it's usually not a cardinal sin. DH+ can take a lot of wiring abuse before it fails, so in the case of failure everything should look textbook.
Termination resistors
All networks must have termination resistors at the two physical ends of the network (in the Station connector boxes in the case of trunkline dropline, or on the nodes themselves with daisy-chain) . Some devices (Classic PLC-5) have internal termination resistors that can be activated by dip switch setting so the absence of a physical resistor doesn't mean it's not there.
Links at 57.6k or 115k with "older devices" should be terminated with 150Ohm resistors.
Links at 230k, or where the whole network is newer devices (basically anything capable of 230k like DHRIO and PLC-5 Enhanced) should be terminated with 82Ohm resistors. I've seen a note that 1756-DHRIO can work better with 82Ohm if the network can support it.
Troubleshooting
-Check for stray wires potentially shorting between terminals and resistors, and loose connections. I've seen DH+ and RIO mostly work when one connection was completely broken on the blue or clear, and others where it mostly worked when terminals were not near tight.
With a meter on Ohms you should measure the following:
-Very high impedance between shield, and either blue or clear
-What may appear to be a short between blue and clear.
-High impedance between ground and any of the connections.
Station connectors capacitively couple shield to ground. Shield could probably be solidly grounded at one point only, but this isn't called for in the standard. Clear and Blue should not be grounded, nor should have any voltage on them (a stray connection to a 24V or 120V supply).
If you measure a short between shield, and blue or clear, you may have a crossed wire at a node. I've seen a DH+ that worked for over a decade at 57k with a node that had clear and shield (using clear heatshrink!) swapped, but caused problems when the speed was increased to 115k. The DHRIO card on that network would become slower, and slower, and slower, and stopped responding. Both the LED display, and through RSLinx! Is your node with a malfunctioning RIO a 1756-DHRIO card on your DH+ or a PLC-5? PLC-5 seems very immune to problems on other channels, though the above problem could make the entire DHRIO malfunction.
A DH+ node powered off and disconnected from the network will measure 8 ohms (or is it 4?) across clear and blue (1 and 2). Your whole network with all devices' 3 pin phoenix connector unplugged should measure the parallel equivalent of the two termination resistors between blue and clear, and nothing between shield and either blue or clear.
Ron explains how to look at Active nodes in Channel 1A of a PLC-5. If you have a PLC-5 enhanced set a channel status file. The same active nodes are hidden in the data table but useful if you're on a channel other than 1A, and it will also show retries, etc that can show the relative health of the network.
Advanced Troubleshooting
A 1784-U2DHP can be used with the software "NetDecoder" to analyze packets on the network, but it sounds more like a connection issue. However Netdecoder can highlight issues like hammering messages that could overwhelm buffers on certain devices.