You probably need to fit a diode to the relay coil connections (green & blue) to prevent the high voltage kick as the relay operates and releases from damaging the decoder. May be a bit too late now though.
Hornby sell power clips and power tracks that are specifically for DCC use and don't have suppressors in them. Those clips and power tracks that do have suppressors in them can be prised open to allow the suppressor capacitor to be removed for DCC use.
It's CVs 54 and 55 that need adjusting to eliminate jerky starting and stopping.
CV 54 affects starting and CV55 that controls stopping. There used to be a chart with suggested values on the Bachmann site but it seems to have been taken down since their website was updated.
If the point motors are screwed to the baseboard, try loosening the screws very slightly. Overtightening will cause problems.
PS. Some Peco CDUs are a bit weak, early ones especially, later ones are saidto be better.
With any ringfield motor, you have to ensure that the left hand brush strip is isolated from the chassis and wheels. Failure to isolate can (usually) lead to immediate decoder failure when power is applied. There is a section on Brian Lambert's website that covers ringfields.
30ma is usually quoted as the maximum that LED can take but it is far better to run them at a lower current to prolong their life. 20ma or less would be better.
A 1k resistor in series with the supply is a pretty "normal" value if the supply is 12volts.
Acetone should soften super glue if you can get it to penetrate the screw threads. Problem is that acetone attacks some plastics!
Another thing that may help is to heat up the tip of an old screwdriver and use that to try to undo the screws.
Those wheels look quite thick, so it may work better if you reduce the back to back down to somewhere near to 13.9mm, which was the standard that Hornby used in the not too distant past.
These sound like the old Hornby Zero1 decoders which are totally incompatible with DCC.
See http://www.kingstrains.co.uk/Hornby-Zero-1-Loco-Decoder-Chips-Pair