Not exactly sure how to get the gear back in time. But just having the tie rods off shouldn't have had anything to do with it getting out of time.
There is a gear slack adjustment screw with a jamb nut on each side of the gear box. I don't know if backing that screw out would give enough slack to get the gears out of time, or back into time. Possibly one has come loose and backed all the way out? Something to check before going into the gear.
But for one arm to move, and the other not, sounds like something is very worn or a broken tooth on a gear. If there is a broken tooth on one side, you should be able to feel it skip when the missing tooth goes by the pinion gear.
When the arms are properly timed, with the steering straight ahead (turn the wheel lock to lock, count the turns, go back 1/2 way), the ends of the arms should be aligned just above the top bolt that holds the radius rod ball to the case.
You don't need a pickle fork to get the ends off. A pickle fork will work, but guaranteed to ruin the boot. Try this, loosen the nut, but leave it on to protect the threads. Hold a big hammer or block of steel against the front side of the sector arm, where the end stud comes through, use another big hammer and wack the opposite side. What this will do is squeeze the tapered hole slightly and pop the stud loose. You may have to hit it several times, helps to put some pressure with a pry bar while you hit it.
To set the toe in, first the steering gear needs to be right, so this will be the last thing you do after getting the gear repaired and the gear lash adjusted.
Again, do the "center the wheel" count. This is important so once the adjustments are made, you will get full turning range, both ways. Tie the wheel, or get some reference in case it moves during the procedure.
Tie a string to the draw bar, pull it tight around the back if the rear tire, centered with the axle. Extend the string to the front, past the front of the front tire. Hold it tight and move the end of the string left and right until the string just touches the front of the back tire. What you are doing is establishing a straight line down the side of the tractor. Tie the string to something heavy you can move back and forth to hold the string tight, just touching the front of the back tire. Do the same for the other side. Hopefully the front axle is set narrow enough for the string to be outside the front wheels, if not you may want to set it narrow enough for the string to clear the wheels.
Next, take measurements from the front and back of the front wheels to the string. Adjust the tie rods until the wheels are parallel with the strings. If you want to give it a little toe in, set the front about 1/8-1/16" further from the string.
Take your time, check and double check each side before locking down the clamps. Of course the condition of the tie rod ends, spindle bushings, wheel bearings, straightness of the wheels, radius rod ball and sockets, center pivot, steering knuckle clamps and keys, all have an effect on the alignment. But, this isn't a race car, just get it close and all will be well.
Hope this helps, let us know...