1996 Honda Civic weird trans behaviour

Uh oh.

1996 civic 1.6 SOHC manual transmission

Bought it as an insurance salvage car had the ignition punched out, and a bad cv axle.and no speedometer.

Anyways. I drove it home 50 miles got it to my shop turned it off and didnt get the third click, battery drained.

I replaced the front driver cv axle, speed sensor and ignition switch.

Jumped the car off, it will start and run. But after a short time it dies, appears as if maybe a weak alternator. But the real problem is the car refuses to go into any gear now when running. It idles fine just as soon as trying to put it in gear it gets weak and dies.

I cant think compression problem because I drove the car at 80 mph.
I tend to think alternator because of how the gauge lights dim, but cant see how that would keep a manual transmission from going in gear.

The only other thing I can think of is clutch, but the pedal feels fine.