Why does my transmission flex while under load in 1st gear? I guess its the transmission and motor flexing around as load is applied. This happened after I replaced a torn apart transmission mount with a new one. The motor mounts are in good condition.
If I'm off road or just climbing over stuff (rocks on a trail) the clutch makes a worring noise.
Everything moves less in 2nd gear and nothing in 3rd.

I think your working with a Yugo (didn't say what you are working on so I will go with a Yugo) I would take a pry bar and start checking your motor mounts and and trans mount sounds to me like one is broke

Oh I'm sorry 1988 samurai.

The stock rubber mounts will allow alot of movement, they are not solid so thusly provide at least a half inch of play when torqued.

I understand the movement that comes with the rubber, its no urethane, nor does it need to be.
But this is way to much movement. A completely separated (old) tranny mount didn't allow for this much movement. The shifter moves maybe 3inchs so maybe everything is moving half an inch or so. But the clutch really lets out a whine under some good load. This shouldn't be.
I guess I'll just ghetto rig it and put a block of wood between the transmission and transmission tunnel. Awesome!

Never mind, I'm just a moron. Driver side motor mount has been sliced. I was unable to see it but started pryin around with a crowbar and found it.

Glad you found it,