MANDALAY
Worked out how to bolt it down by welding some steel to the engine bracket for a solid mount. Double checked the clearance and looks OK
Solid mounting the intercooler to the engine block is going to transmit vibration to it that could prove destructive over the long term. Inline four cylinder engines (without balance shafts) exhibit a strong second order vibration in the direction of piston travel, and at high RPMs this can literally shake to bits anything solidly fixed to the engine. It's likely to manifest in an intercooler as fatigue cracks that could cause small water leaks into the induction air or externally, or external induction air leaks.
The factory manifold bracing is there to prevent sympathetic vibration and eventual failure of the manifolds due to this - it might seem like overkill but is quite essential to reliability.
I used rubber cushioning grommets to mount my intercooler, similar to these:
I fabricated a solid bracket to mount the intercooler, then used the grommets to cushion its mounting to the lugs on the head casting:
The intercooler is quite free to rock forward and backwards with this setup, and the final support comes from the silicone hose to the throttle making it firm but flexible. Most importantly, the destructive high frequency second order vibrations are damped.
If you intend to keep this setup for a while, it's probably a good idea to do something similar especially considering you're making custom end tanks for the intercooler.