can d2 engine run alone?

If the complete clutch parts of the master clutch is removed down to the flywheel there is no reason why you can,t run it.I have ran dozens of them on the dyno and you have nothing hooked up except the shaft to the dyno but that wouldn,t mean any thing if it wasn,t hooked up to the dyno.

abram - There's no reason why you can't run the engine out of the tractor chassis - but make sure it's properly held down or anchored in some manner, so that it doesn't fall off the supports you have under it, or fall over.
I'd be fabricating some engine supports welded to a length of steel, back and front, and bolting the engine into it.
I ran up an automotive 6 cyl Perkins Turbo Phaser, sitting on a stand-alone basis, late last year, and I had a little trouble starting it, because I forgot about the need to electrically energise the fuel shutoff.
When I cranked it after energising the solenoid, it started and roared into life so fast, it amazed me. An engine in good shape will fire up instantly, within a couple of revolutions. Make sure your exhaust fumes are properly vented, and don't gas yourself.

If you don't want to go to the trouble of building a stand like you should, at least keep whatever hoist you pulled it out of the tractor with, hooked to it with all the slack taken out of the lifting shackles. That way it won't go far if it vibrates off the blocks etc.

I ran the D311 out of our grader quite a bit on blocks, making sure I had good oil pressure etc before I put it back into the frame. I was most in danger of having an accident when tightening or loosening fastners etc.

A quart can with a line dipped into it will take care of fuel.

I've run lots of small block chevies sitting on the ground with nothing but a battery and a can of gas and holding on by hand, got to watch it when you goose'em though, they will try and fall over. Just acquired a pair of Detroit 16V 92s with twin turbos, won't be trying to hold onto them by hand when we hit the starter on them.