To protect the bolts from resin I just covered them in grease and they came out easily. For the resin you want something with the lowest viscosity you can find and a long setting time, to maximize the chance it has to self level. I'm not sure if the viscosity of polyester resin will be low enough, probably not? The resin I used is west system 105 with 209 hardener.

Don't concern yourself too much with the weight of the gantry. What's more important, to have a strong machine or a fast machine? Your answer is almost certainly the former, so make it as strong as you can and then worry about possibly needing a bigger motor. Since you've already got the motor you might as well try it, but 3Nm is a bit on the small side. If you got another of the 425 oz-in motors and drivers, then connected one to each X-axis screw you would have enough power to move (at least) a 50kg gantry at a decent feedrate and acceleration.

Shame you got the 1.5kW spindle not the 2.2kW one. The 2.2kW spindles come with ER20 collets, so instead of holding up to 10mm tools they can hold 1/2" tools. That's useful if you want to use cheap router cutters.

Generally putting the rails on the part of Z that moves up and down reduces the overhang, i.e. the distance between the tool tip and the linear bearings.

Have you done a drawing of the gantry? It's a bit late now but it would have been easier to make a strong machine if you'd gone for an adjustable height bed and had the Z-axis working below the level of the X-axis rails, like in my build logs. Still, if you're not planning on cutting metals then you'll get away with it.