After milling the head and sinking the intake valve by the same distance, some adjustment must be made to recover the valve train geometry.
Shimming the rocker stand corrects the rocker-to-intake-valve relationship, but causes other problems:
1. the intake pushrod is now too short, and may be out of adjustment range.
2. the rocker-to-exhaust-valve relationship inherits the .090" error, in reverse.
Assuming the other dimensions are correct, the easiest fix is to remove .090" (or whatever mill-and-sink distance you used) from the intake stem tip + slightly more to allow a lash cap to be used to protect the softer tip; use whatever the mfg. gives as the cap thickness (not the height) here such as .060".