Building up a Rock Lobster tig team SL as a cheap but half decent MTB for short blasts after work.

My issue is that in the 2 lowest gears the chain is riding up on the edge of the lower jockey wheel, making a racket.

The drivetrain is:

Shimano Deore HG53 9 Speed Chain – new
Shimano 9 speed casette – 2nd hand but good condition
Shimano LX mech (dark grey) – 2nd hand, new jockey wheels fitted by seller
Shimano XT M770-SLX M660 Bottom Bracket – new
Shimano LX cranks
On One SS chainring

I have 1 spacer on the drive side of the BB (2 on the non drive side) and the chainring mounted in the middle position, it seems fairly central, but as you’d expect, there is a less than perfect chainline in the lower gears. My first course of action will be to swap the spacer over to the non drive side, but I’m not sure that this will sort it out. Any other thoughts? different jockey wheels?

You have your spacers on the BB the wrong way round. You need 2 on the drive side and 1 on the non drive side, as the RL will have a 68mm BB shell. Def don’t move another spacer to non-drive side. With the spacers in the correct order, the middle ring position will be central for the chain line, and your pedals will also be central. If all spacers were on one side, they would be off-set to one side.