This might not be the solution you are looking for, but this is how I managed to make my Tomcat have the correct missile firing sequence, and I know other users have been plagued by this problem in the past.

The problem is nobody really knows how weapon sequencing works in SimplePlanes, it's basically black magic, it seems totally random.

This is the initial firing sequence of my AIM-54 Phoenixes on my Tomcat build, which I am still improving steadily. Obviously I don't want it to fire crisscross like this as it would not have happened like that on the real plane.

So my solution was I used the Fine Tuner mod to multi-select one whole missile assembly at a time, and swap the two right hand fuselage missiles front-to-back. The oddity here is that the one in the back is technically connected to the pylon in the front, and the missile in the front is connected to the back pylon. When I tried attaching the missiles to the actual adjacent pylons, it undid the firing sequence and went back to crisscross.

i.e, it ONLY works when the physical connections are UNCHANGED and the physical position of the missile is CHANGED

This was the final desired sequence, which it now keeps. Jettison functions have been unaffected.