Will a 3.1 from a 1992 Rodeo fit in a 91 trooper that has a 2.8?
Questions that come to mind. Motor mount match. Transmission bell, flex plate to clutch plate? Computer harness?
Trooper is manual 4 wheel drive. Rodeo is automatic 2 wheel

 

You've got some challenges.

The 60° GM engines for an automatic will have some differences where going from a manual to an automatic block. Some of the tapped attachment points won't be finished.
When going from a torque converter to a pilot bearing, some cranks won't be machined to accept the pilot bearing. All the crank register does on an engine for an automatic is center the torque converter. That doesn't require a machined register. The pilot bearing does.

Both engines use the same bolt pattern for the transmission.

The 3.1 makes better power. Another option would be to look for a manual transmission 3.4L GM engine. A possibility would be from a camaro.
The 3.4 makes considerably more power. The cam should probably be swapped for an RV type for more appropriate torque.

Is your 2.8 too far gone for a rebuild?

2.8 to 3.1 I wouldn't be too concerned about harness and so forth. 3.4, might be another story.

 

So if a GM 4.3l should have the same bell housing too? A 4.3 is the same bell as a 5.3 or smaller chevy.
If I am wrong someone correct me please. I need another engine but don't want to put a wimpy 2.8 back in.