how bad was the filter -- could there still be crap in the fuel system or the injectors clogged?
I wouldn't necessarily trust injector clean. You may need to pull them and get them done properly, or at least test them on the bench.
For smoke test - take off your filter box and MAF and block the post-MAF intake with something suitable. Typically a tin can with some smoking cloth in it and an air nipple mounted on it. Pressurise to ~1bar and look for leaks.
Your idle problems, the fact it gets better if you induce an intake leak, cold vs hot, still sounds a lot like an IACV problem.
Did you get around to changing the o2 sensor yet? Have a look with the scan tool (or any SSM device) at idle and make sure the o2 signal is flipping back and forth.