the power steering pump's plate that 'hangs' it on the block...is different...you may need to use the stock FS-DE's power steering pump bracket instead, so it may involve finding one at a wrecking yard or parts store...shouldn't be too expensive, but iirc the holes in the block won't line up correctly with the MSP's bracket...
Its more confusing in writing than if you just do it...as the parts you need from the msp engine are probably fine to swap over to the standard 2.0L protege engine...
The mechanical differences are small...the crank cradle, or 'girdle', or windage tray (the plate that mounts above the oil pan on the bottom of the block) is tapped for the turbo's oil return line on the MSP...so you need to use the MSP's tray, instead of the normal protege tray...If you don't want to do that, then other guys just tap a hole in the pan for the return line...it accomplishes the same thing, but the pan being stamped and pretty thin...makes it difficult to get a full proof seal for that line...the tray on your msp engine is probably perfectly fine for the swap though; they're not overly under stress or anything unless you grenaded the entire engine...
the MSP also uses an oil cooler adapter plate that routes coolant...and cools oil moving in an out of the oil filter by mounting between them...you'll need to keep all the coolant lines and the plate itself to swap it to the new engine...
the cam shaft gears: That is a matter of what specific FS-DE you are using; meaning what car it came from...the FS has been around a while, but lots of little changes were made over the years...Your MSP computer needs to have an engine with the cam position sensor reading the exhaust cam gear...not all FS engines have cam gears, or a valve cover, designed for this...if you pulled the engine from any 3rd gen protege...you have nothing to worry about, but if you pulled it out of an older car (especially one with a distributor), you'll have some work to do...You'll need to use your MSP valve cover, cam position sensor, and cam gears...your MSP crank pulley and crank position sensor also (if the head is different, chances are it uses that eliptical crank gear instead of the MSP's 'teeth')...and even worse, if you have an engine that was distributed...you'll need to find a way to plug the front of the head where the distributor shaft comes through...
good luck man...