Transmission not shifting properly after engine swap

Hello,

I recently blew my engine on my car listed above GT model. So I got a new engine that had the same transmission in it as my car. The engine came with a new clutch kit already installed so I had no reason to get a new clutch. The transmission I was going to bolt to it had a clutch that previously would grind into all gears and it was very difficult to put it in first and second gear. So I removed the old clutch and the new one and compared them and the old one looked toast. So when I put all the components back together I didn’t have a clutch alignment tool so I had to leave it in the transmission attached to the throw out bearing and clutch fork and screw down the pressure plate as I put the transmission on the engine. So when I started the car everything worked fine but when I put it in first it’s as if it were still In neutral and the same for all the other gears. I took the CV axle out and turned the crank to see if it moved and it doesn’t move at all when the crank is turned. Anyone have any advice?