I did a trans flush on my tj today, the old fluid was like mud and there were some metal shavings on the bolt magnet. After emptying the trans I disconnected the cooling pipe to pump the old fluid out of the torque converter while putting in new fluid through the top. After I had gone through two 4 litre cans of fluid and fixed everything up I started the car and put it into drive, however it did not engage at once instead it slipped, engaged and then disengaged completely, this happened about twice when I backed it up into the garage. It also made some clicking noises. When I stopped the engine and checked the level there was not enough fluid. I will buy some more fluid tomorrow but until then what do you guys think?
Has the transmission had it? It worked perfectly well before this , but since I just got the car and the fluid was extremely dirty I decided to change anyway.

Has the transmission had it?

Doubt it, but you won't know until you get the level right. I hope you are putting in the genuine Mitsu fluid!

Not the genuine one used castrol transmax multivehicle (tqm st), closest thing I could find to dia queen 3

You need to put the correct fluid in. I had a Toyota that was designed for Dextron 2 which is harder to find nowadays and the tech guys at the oil company said to use Dex 3 but it would be slighly harsher. Not only was it harsher but it failed to change gears when it was cold. Eventually it completely clogged the filter with clutch friction fibres. I flushed it all out and put Dex 2 in and all the problems went away.

Also, you must measure the oil with the engine/gearbox hot although you probably need more if it won't do anything. You need at least the 8 litres.

Drain and fill is 5.5 l. Only if you remove and drain the converter is it 8l

Add to this, check warm, in park or neutral with motor running

Get spiii fluid only and get it from mits, is not very expensive

the trans works fine and shifts well after I filled it, and since there was a lot of sludge I will flush it with genuine again at the next oil change.