Good to see you finally got her in there. If I forgot to mention that the upper intake needs to come off for motor & trans install, thats my bad. How close is the steering to the exhaust? You can move the engine over to the exhaust minus 1/2" for clearance, but it looks like your passenger exhaust will need more than that to clear. My flange sits on top the frame, like yours, but there's enough room for the exhaust pipe to clear the frame and trans. You could notch the frame half way without sacrificing strength, could also plate the side for extra strength. Also, the belt routing is wrong, from the water pump it should go to the power steering pump (for more wrap) then to the idler then the alternator...
If I had to do mine again (and I will as I've decided to go with a teksid powerplant), I'd move the trans mount over to the passenger side one inch more for more tcase clearance. The exhaust has plenty of room to spare. It doesnt have to be prefectly lined up with the frame or axle, the ujoints will take up the miss alignment...
SVT