So I noticed there wasn't a really detailed write-up on this site for fixing the shifter on the M5OD-R1/R2, so I decided to do one. It's not hard by any means if you are even slightly mechanically inclined. Also sorry for kinda crappy pic quality, camera was dead and so I used the phone.
So to start, there are several companies that make the kit needed to repair the shifter, Dorman just so happened to be the one I bought, and my local Advance Auto actually stocks the product as a regular item, it wasn't a special order. The Part Number is 917-551, it's labelled as a "Shifter Rebuild Kit" on the box, and as a "Manual Transmission Repair Kit" in the system.
So to start, besides the kit, the tools you'll need are as follows:
T-20 Torx bit or driver
#2 Philips Screwdriver, it has to be a plain #2 Philips, no driver with attachable bits as it won't fit in the shifter boot retainer to get the screws
17mm deep well 3/8" drive socket
3/8" drive ratchet
needle nose pliers
Make sure the transmission stays in NEUTRAL, and chock the wheels and set the parking brake!
Start by removing the screws in the boot retainer, there are four in total, one in each corner:
Once removed the boot, retainer, and foam under it should slide a little ways up:
You'll see the retainer bolt once it's up, one side has a nut on it:
This is why I say deep well, the short one barely fits onto it to break it loose, but anyway, you wanna loosen the nut completely off the bolt:
You'll notice that the bolt is threaded on both ends, so thread the nut onto the shorter end of the bolt/retainer:
Tighten it down and it'll pop out, might take a little force when tightening if it hasn't been removed before, but it'll come out:
This is what will be left once pulling the shifter off the top:
This is where the T-20 Torx bit/driver fits in, there are three screws that have to come out:
If it's as bad as mine was, all the parts will just fall apart once you take the retainer plate off the top:
After pulling the plate off you'll be left with the shifter stub in the transmission:
It's keyed on both sides to fit in the transmission where there are two pins in the tower:
Here is the new parts in the kit:
Two bushings(upper and lower, which are blue in the pic, a spring retainer, two new pins, new shifter plate and gasket, and three new #2 philips head screws)
So, there is supposed to be a lower bushing down here, and after a few years it gets brittle and disintegrates, this is what causes the shifter to turn so sloppy. It also causes you to miss gears when shifting. I constantly missed 3rd and 5th.
Those pins are supposed to be pressed out and the new ones pressed in, problem is, what if you don't have bad pins(which mine aren't) and you don't or can't replace them, how the heck do you get the bushing down there? I have the solution, it is pliable enough to be finagled in under the pins and not damage it.
You'll see there are two notches for where the pins go above the bushing, put the bushing in at a downward angle with the notches lined up corresponding to the pins, the pins should go into the notches anyway like this. Then take the needle nose pliers, stick them into the shifter tower where the end of the bushing is in the hole and pry it upwards a little and it'll pop into place. I've done an M5OD-R2 in an F150 like this and my Ranger, no issues yet!
Put the shifter stub back in:
The flat side goes towards the passenger side which means the keyway goes to the top.
Start the screws one at a time and when all three are in, snug them down:
Reinstall shifter boot:
Enjoy your new, well old but it will feel brand new, shifter!
Hope this helps anyone that has any of these issues, and it doesn't take more the 20 minutes to do it! It also prevents/stops leaks from the shifter tower since you installed a new seal and gasket!