Hi Martyn.
I admit to not using a jig to align anything. Now, that's either testament to blind luck, or as to how good the original kit is.
As you say, the kit frame etch includes fixed holes for round bearings and flat etched spring detail. The kit included the cast hornguides and springs, and it seemed a shame not to use them. To mark out cutting the main frames to accept the hornguides I simply sweated the overlays in place and use them as the datum to cut and file to.
I have had to file back the inside top surface of each hornguide bearing surface on the centre axle to get things to sit properly flat at this stage. I know the suspension would probably cover the worst excesses, but it doesn't hurt to have a square and flat chassis to begin with. I measured the distance from the top of the frame to the bottom of the bearing surface (I'll photograph and explain later), and filed the centre ones down to as near as I could manage.
It seems to have worked. The chassis rolls quite smoothly, there's little sideplay, and I have high hopes it'll be a smooth runner when it's got the motor and gearbox.
Which reminds me, the motor and gearbox I selected isn't specifically mentioned by JLTRT. It is marketed by Slater's as "for JLTRT kits".
The actual one is the GB40S, all metal, spur and crossed-helical gears and Mashima 1824 motor. All I have to do is drop it out of the box, fit it on the relevant axle and wire it up. This is the kind of engineering I like!