This is screaming, "torn intake plenum" to me. If there's a crack/tear in the bellows of the intake plenum, when you apply torque in reverse the tear will open up. This allows unmetered air into the system and will cause rough idle. If the tear is severe enough, the motor will stall.
Any unmetered air entering the system will cause rough idle. Check the common items first. The entire upper half of the motor must be air tight or you will have rough idle.
Valve cover gasket
valve cover grommets
PCV valve and grommet
oil fill cap o-ring
oil dipstick o-ring
side cover gasket
THEN you can start looking for other vacuum leaks. Please read this document.
http://www.sdsysdesign.com/tlc/images/Strife/3FE TuneUp.pdf
The series of hard vacuum lines on the left side of the motor are also likely clogged with carbon deposits and/or debris from the EGR valve and regulator. They have internal diaphragms that disintegrate over time.
As far as the missing O-ring from the FPR, that lives on the delivery pipe to the FPR, not the return feed. I suspect it popped off during removal or you purchased an aftermarket unit without an O-ring installed.
If it is in fact lodged in the delivery pipe, you should be easily able to remove it.
Remember, it's a fuel injected tractor motor with 1986 technology. Always check the simple things first.