It looks to me like you are cutting the engine out of the car (just kidding, dumbass, so don't come and beat me up) and making the engine fit into the crate. It would seem like the best thing you can do would be to cut the engine out and take the engine out. Then put the engine back in and weld the new engine into the crate. I doubt they used headers, but if they did, you should weld them back into place. The engine looks like it is set up for fuel injection.
You can always reach out to your peers – you’ll be amazed of what they can teach you in no time. Not to mention the access to upper management expertise!