interesting machine. Seems to be designed for easy access for laying down sheet material. I'd be inclined to salvage the linear motion parts and made a traditional gantry to save space but that's just me. That leadscrew has got to go. 1/2-10 5 start is the way to go. Maybe even a bigger diameter to cut down on whip. Could you just use a product like super pid for spindle control? I have the g540 kit and it's great but you could try the super pid and if you need to upgrade to the g540 the super pid is still useful.
leadscrew for sure.