I owned a 990 for years. I always wished the tuner was in the receive path. The receiver BANDPASS filters are of course, in the path. There was a mod to put the tuner in path, but I dont know where or what it is (it is not hard to figure it out after studying the schizmo). There is of course is a benefit of having a finely tuned antenna tuner in the receive path, that is; more rejection of nearby strong transmitters, improved IMD performance, etc.
Thank God Yaesu put a "RCA" break in the receive line.
I used this facility to put in VARIOUS pre-amps, preselectors, bandpass filters, to customize the excellent receive capabilities of this radio. I however dumped this fine radio due to constant annoying White Noise (hiss-s-s)in the IF/AF chain as documented in the ARRL review. See my FT 990 review here in EHAM !
Ken, WB9YCJ/6