So made a new brace and fitted 15mm further back;
Filter now fits over the intake stack;
Battery is a tight fit, especially as I'm planning to use a 'Motobatt' which is 3mm thicker than the Yuasa but it clears the underside of the tank, although I need to lift it around 10mm to clear the rocker cover but as long as I'm careful with the battery box dimensions there should be no issue.
Next step to strip down to bare frame to get the welding finished and frame blasted/painted, although probably do another test assembly first just to be sure.