The FS and FE are both relatively similar in deck height...the heads are different, but i doubt enough to cause a hood clearance problem...the real problem is the FE is extremely long compared to the FS...in fact, the FS name came from 'F series SHORT'...it was designed as a shorter block variant of the same engine family...
The big issue is the FS and KL's were designed for the exact same front sub-frame...that sub-frame never housed an FE3...so most mounting points would need to be custom...that isn't impossible by any means, but it adds very considerable work over a KL swap...which is literally a drop in affair (other than AC)...and most of the hard work is in wiring...which you would still have with an FE3...
Many Mazda guys refer to the FE3 as the best piston engine Mazda ever made...even more so than the BP...both of which are found on numerous 'best 4 cylinder engine' lists...but the FE3 was literally built as a small truck engine, designed to be planted 'normally' for a RWD car...the FS was designed for the opposite purpose...obviously Mazda still put the FE3 in some FWD's over time, but it used a radically different front end...all of which would have to be researched and handled properly in order to work...
I'm speaking in terms of 3rd gen proteges, though...Tweety may have many more options in that department than 3rd gens do...