A little back story. Since I have received my truck (1997 Ford Ranger 2.3L 2-wheel drive) I have had some troubles shifting. I was having issues shifting into 1st and 2nd gear, grinding into first almost every time (felt like I was hitting something and then sliding into gear) having it pop out of 2nd gear when going up hill, and when shifting into reverse having the entire truck clunk into gear. I had the fluid swapped out twice, once by myself and another time by a shop that flushed everything in my transmission and replaced the fluid. Nothing was fixing the issues so I proceeded to have the clutch swapped. When they swapped the clutch, they did the works on it machining the fly wheel and rebuilding my shifter, "inspecting" everything along the way. When I got the truck back my clutch pedal only engaged about an inch from the ground and had about 2-3 inches of play before even starting to feel like it was going to engage and the 1st gear issue was still present. Pretty sure they never took it for a test drive even though the said they did because my odometer only went up 1 mile from when I dropped it off. Brought the truck back asking if they inspected my pilot bearing when they did the swap, which they said they did. They bled the clutch and said that was all that was needed, and to give it some time before bringing it back, Issue still present but I had to deal with it as I was leaving the week after. Same time I had everything looked at to make sure I would have no issues driving 200+ miles. They said everything looked great and said I should have no issues.

Day of the trip I make it 40 miles away from my house and something happened. Cruising at 75 mph, I lose 5 mph in a second with my foot pressing the pedal to the floor in OD. I noticed this wasn't right but by the time I could react I hear a clunk under my truck, smoke coming from below my shifter and it pops out of gear. Unable to go into any gear I come to a stop and wait a minute before trying to shift. I am able to shift it into 1st gear, but hear a whiny noise as I am driving in 1st-3rd. I get it into 4th and it drives fine enough to get it to a gas station where I have it towed to the shop, thinking they had some shady practices and caused the damage. I had to press on to Mountain Home so my wife dealt with the shop. They told her the "front output shaft bearing" failed and the transmission was shot and would have to be swapped, but were able to get me a deal on one. 1k for tranny and install, while another company was taking care of the other 2k because somehow the part that failed was swapped out when they replaced my transmission fluid the months prior.

Now I have issues shifting into 2nd gear like I had shifting into 1st, but it sounds like I am hitting a gear or some metal.
Sorry for the long paragraph, but I am not mechanically inclined when it comes to cars at all... Does a 2-wheel drive car even have a front output shaft? I thought that was for a 4x4 with a transfer case? Any ideas on what was originally wrong with my shifting/now?

 

Seems like a synchro issue to me. It is possible that they're referring to the bearing on the input shaft or on the counter shaft on the front of the transmission.

 

Welcome to the forum

You have an M5OD-R1(M5R1) manual transmission, very reliable transmission but did have one rare flaw, the input shaft gear

You will need to get a use M5R1 or rebuild yours

M5R1 has integrated bellhousing so even though 3.0l and 4.0l Ranger use the same Model transmission, that can't be bolted to the 4cyl engine

So for used you need one from 1989 to 1997 2.3l Lima engine Ranger or Mazda B-2300 1994-1997, 2WD of course
After 1997 there will be no speedometer cable port on transmission, which you need


What has happened is that the input shaft gear has stripped inside the transmission, the only gear that doesn't use the input shaft gear is 4th because it is a 1:1 ratio so input and output shafts need no "gear" they are just connected directly together

Image of input shaft here: https://i.ebayimg.com/images/g/0GIAA...fA1/s-l640.jpg
The gear is inside transmission the shaft sticks out into the bellhousing, the splines are where clutch disc sits, and end goes inside pilot bearing

Here is image of the gear setup for 1-4, no 5th or Reverse: http://www.nationalnewstoday.com/wp-...enfeld-10b.jpg
Upper left is the input shaft, its gear is stripped and damaged counter shaft gear as well
4th gear would have work in this transmission, but no other gear

A used M5R1 is not a bad gamble, there were literally millions of these installed from 1988 to 2011 in Rangers and B-series pickups, with very few coming to this type of end
Local wrecking yard should be able to source one, there were alot of 1989-1997 2.3l Rangers built, most were 2WD with manual transmission(M5R1) because of the better MPG which was the point of getting a 4cyl engine
2001-2011 2.3l Ranger trans will NOT fit, its a different engine, a Duratec 2.3l


EDIT:
I re-read your post, so shop already swapped out transmission, with used, and you are having shifting issue again
This would be almost impossible to get 2 M5R1 transmissions with something wrong inside, it could happen, like winning the lottery, just not very likely

What the history on this Ranger, was it ever in an accident?

It is possible the engine dowels and bellhousing are not lining up, which caused 1st failure and now the 2nd, so transmission is not the problem its the SYMPTOM of the underlying problem
When you are dealing with shaft speeds of 1,000 to 6,000RPMs any little off-set can cause BIG problems
So the crank shaft(in the engine) and the input shaft in the transmission MUST BE LINED UP PERFECTLY
If they are not then you get a vibration and the input shaft and bearing get the damage

The engine has dowel pins(or sleeves) that the bellhousing slides on to, these "should" align the shafts perfectly
This alignment can be tested when transmission is off

 

I cannot express how appreciative I am of the in depth answer! Your post gave me more information than a years worth of googling. The truck has never been in an accident, but it did sit for a few years in a driveway, being driven once or twice a year to make sure it still ran. It was a relative's truck that was unable to drive.
I am out of state from the shop that did the transmission, but I will bring this up (and pretend like I know what I am talking about with confidence) when I am back in town. They ops checked it by driving it one mile and calling it good I found out as well...

 

RonD. I have a '91 Ranger 2.3L manual. I have 170,000 miles on it. It shifts perfect. Should I be replacing my input shaft gear as a preventative measure?

 

No

While this is a "known" issue its not a common issue by any means
Just change fluids at service intervals

 

Thanks.