Many congrats on your acquisition and successful completion of this wondefrul project vehicle. As others have pointed out, this is a great platform for both stock restorations and some over the top stuff alike if you fancy so. A few observations that i have made are as under.
1- Your AC compressor is on the wrong side of the engine and i dont see how it can fit there unless some custom mounting plate was fabricated. All the, the stock AC mounting is on the right side of the engine and accommodates both the power steering pump and AC.
2- The gear boot in the second photo is too stretched vertically, which leads one to think that either the wrong gear box mounts have been used or the cross member at the bottom on which the gear box sits is deformed. Another reason could be that the gear lever was cut/weld altered to 'zabardasti' fit in the wrong mounts( dont be surprised if it is, a guy tried to do the same with me during my early FJ days instead of rejecting the mounts). If the powertrain is mis-aligned in such a way, with such a heavy engine and open diffs in cross axle situations with crow hop, you will find yourself frequently buying new mounts for the engine and gear box.
3- Your tires are great, yoko geolandars i take. But the width they have will give you body rub inside the wheel arch when you flex. Not only will that limit travel of your wheel, but will also damage the body.
Please dont take these observations/comments to be negative in anyway. I just thought id share these points with you to make it better according to my own understanding, which is rather limited by all standards. Stay safe and happy wheeling!