I always use the Nut and bolt method, i use the springs from the original plastic clips, tighten down so the heatsink can move and the springs are even as they were under the plastic clip downs. just don't tighten down fully as you cant tell if heatsink is even across NB and risk damaging NB chip with to much pressure on one side.
The delta between NB diode is also variable, depending on where and how well the thermal temp sensor is glued to NB heatsink, I have seen people say a delta of 10 means good contact but have found this can change with different NB heatsinks depending on temp sensor mounting on said heat sink.
You can add extra cooling to the NB and ram using this method i did a few years ago. it works and keeps temps down nicely.
Some extra cooling makes a difference 5.1pro | MacRumors Forums
As for CPU mounting in a 4.1 dual CPU tray delided CPU's are better but can be done with out deliding the CPU useing a 1.5mm shim washer over mount posts, make sure its a shim washer not a stamped out washer from your DIY store. you can even mount them with no washers but if you over tighten the heatsinks you can damage the socket and pins.
If you find the red cpu light comes on its most likely to tight and pins are not touching CPU. if you look at the socket the cpu should touch the pins just by placing in socket as the CPU itself is against the plastic edge of the socket mount. over tightening the heatsinks pushes CPU hard against plastic edge of socket mount literally bending the CPU mount and board itself and as we know the traces from CPU are in the board and copper traces dont stretch inside the cpu board itself they break and render the board useless.
I would inspect the socket pins with a powerfull magnifying glass to see if there is any pins that are stuck down or bent. you can straighten the pins if your very careful useing a dentist pick tool. if you use alot of thermal paste when mounting as it squeezes out making the mounting screws become loser which can also give you a red CPU light. a light even spread of thermal paste is the way to go.
Mac pro 5.1 cpu tray is much easier to replace the CPU's because the heatsinks tighten fully after doing half a turn on each in a cross over pattern 1-3-4-2 and back again untill tight. you also have the CPU lock down tray around the socket. if the red CPU light comes on either CPU not mounted correctly or duff CPU but if proven working then socket pin damage or some times even CPU's mounted the wrong way round and clip forced down. even the back of the cpu might have debris or dirt on it, clean with alcohol before mounting cpu in socket making sure the CPU is placed straight down taking care it located in the right way round with the little notches in cpu lining up with the socket.
I hope you both have success with your CPU boards ?
