I have a 1988 Ford Ranger 2.9L 2wd and it's a manual, and I was driving home on the highway one day and heard a loud whine from the truck and the truck died so I pulled over and the truck was like locked up wouldn't start finally got it to start with truck in neutral but when I released truck in neutral it acted like it was in gear and would die every time, we checked the clutch and slave cylinder and they was both working fine drained the gear oil and noticed there was very little in it, so as of right now anything would help me

 

Trans is bad
Good news it is an M50D-R1, '88 was the first year they were used in Rangers and they were used until 2012, so you won't have a problem finding a used one.
2.9l uses the same trans bolt pattern as 4.0l OHV(or SOHC).

You can rebuild it but contrary to what you may be feeling now the M50D-R1 was a super reliable transmission, so used isn't much of a gamble if trans fluid smells OK.

You may be able to move it in 4th gear, as that is a direct path thru trans, but really depends on what broke inside.

The whine was from a gear being chewed up, input shaft gear is my guess, probably from low trans fluid.

If you have never rebuilt a manual trans M50D-R1 is a good one to do, but really up to you.
Used trans will, in most cases, be cheaper than rebuilding it yourself

 

Thank you so much I believe it is input shaft, the input shaft won't spin in neutral at all and we have found one BB from a ball bearing so far

 

The trans oil smelled really strong and was a terrible smell is that a sigh of anything?

 

We got the input shaft to spin and all the gears inside look like new the only thing we can see is that the sliding gear for 1st and 2nd doesn't spin with the rest of the gear shaft

 

It was distilled, boiled down because of overheating, so strong smell.
Manual Transmission fluid doesn't normally need a cooler like automatics do, because it doesn't generate as much heat and has a large enough capacity of fluid to distribute that heat thru natural circulation.

When fluid gets low then heat builds up, and parts start to run warmer, you get to the point where parts are hot enough to cook the fluid that does make it to them, instant boil, like throwing a drop of water in a hot pan.
And that's when the trouble starts

 

That is the Dog gear, one of them, it should be connected to output shaft, and should not spin with input shaft unless it slides over to connected with 1st or 2nd gear, that is how a gear is engaged, the Dog gear has the syncromesh on either side, when it slide over to 1st gear it must match speed of input shaft(1st gear spin) to speed of output shaft, the syncro helps it do that quietly.