99 Dakota manual transmission won't go in gear

Failed transmission is likely.

Your transmission is the 42RE, formerly A500SE, and A904 way before that. Due to the electronics involved, you would need the computer and associated harness for a manual Dakota if you were thinking about using a non-electronic automatic.

Check and/or change transmission fluid and filter. Retry.

No the fact that your vehicle is low on gas should have nothing to do with the shifting of the transmission. You are dealing with two separate issues.

Most likely solution is the gear selector fork in the transmission has broken and is no longer engaging the gears.

Repair requires transmission removal and partial overhaul.

You will probably need the ECM and all the electronics unless you have a 3.9 in your 99. The Engine management will be different. as will the transmission and powertrain computers of each truck(2vs4 wheel drive, different differental gears). It is best when doing a swap to have both vechicals in case you need something else. Then you need patience and extra cash.

oil to thin filter not cleaned? hope this helps?

75W/90 gear oil.

clutch needing replaced, very common on all manuals

pedal travel adjustment,yes
gear shift adjustment,no

either repair or replace the transmission...sounds like the sensor went out