There are a number of things you can try :
Your ignition timing table is quite relevant to what the IAC algorithms can do. If 900 rpm is your target for hot idle, then add a column at 900 (right click 700 column heading, "insert") and set the advance there to what you really want at idle. From your log it seems it's at 13 degrees while keeping a steady 900 rpm idle. Set all cells in the 900 and 1200 column, 46 and 30 kPa row, to 15 degrees. Also set 20 degrees at 700 at 66 and below. This gives a natural advance that should work with just a throttle stop and no idle air valve with PID control.
Enable ignition advance control as a last measure, give it +/- 5 degrees control, IAC threshold to 4 degrees - it calls on extra air if more advance change than that is needed to maintain target idle rpm. I usually set the rate to 25 degrees/250 rpm to get a lightning fast adjustment.
I'm not sure 250 Hz is the correct frequency for this valve, try lower like 50-75 Hz.
Under PWM Idle control dialog, set reasonable max/min allowed duty values, if you idle well at 40% then set the min value to just below like 39%. If a hot summer day with hot MAT readings requires more, cure that with tuning the "refpos addition for MAT, slope".
You should look over your IAC duty % while cranking, 10% cold and 100% hot is not always the best situation. Try using your hot idle duty % for both hot and cold to start with.
I usually use a couple of % higher duty in the ref table, and use more "integral decrease" (and basically no "increase"). That way the valve closes to keep rpm down, rather than the opposite.
Don't do it all at once, try to be systematic when going about this. I would start with a decent ignition table. We could really use a separate ignition advance table, hopefully in a not so distant firmware revision.
BTW, your MAT/TPS fuel enrichment table is all shot to hell, replace it by drag'n'dropping one of the default firmware configs on the table for that dialog. You currently have very poor compensation for the basic natural laws, cold air = more fuel, hot air = less fuel.