The rattle in the E string is still gone, the A is slightly there, it only shows up if I really dig in. It also can't be heard if I'm plugged in.
If what you have left is a "rattle" on the A string only, it's likely due to insufficient break angle at the witness point of the nut.
Try this: play an open A and then use your fingering hand to gently press down on the A string behind the nut. If the "rattle" goes away, it is not rattle, it is sympathetic vibration of the "non-active" portion of the A string behind the nut. More wraps to increase break angle behind the nut are needed. But do not double-wrap the strings on the post. Simply cut the string so that you get a full post of wraps on the A string to maximize break angle.
And BTW, you do not need a capo to check neck relief. Simply fret low F on the E string normally, and then use your other hand thumb to fret the highest note on the E string. Then rotate your wrist and stretch your pinky back toward fret 10 on the E string. Fret the E string with your pinky and see how far you need to tap the string down. Anything more than a credit card = truss rod adjustment.
