Dont worry about the port mis-match. Get the engine, 360 or what ever it is. Put it in and run it (put the 352 4 V on it you want or not.) Then you can rebuild the 352,
I will comment that you will need to contact someone like Barry Robotnic at
www.survivalmotorsports.com if you really want to make a 352 or a 360 into a true 11:1 motor. You will need custom pistons.
My personal opinion, if you use a 352, dont stray too far from stock, those engine RUN SOO SMOOTH, that is a great virtue, dont ruin that. But if you do decide to rebuild the 390, you can get to 11 to 1 much more easily because it has a longer stroke, more cubes for same head CC. Check the date code on the block (behind the oil filter on the tab. Some 390s are low compression truck engines, they will run just fine, but will not be putting out all the beans the can.
You can put all your 352 stuff right on it, and it will look totally stock.
BTW, really cool about finding a manual trans sedan. Great fun hotrod/family car. I have a 1964 500 Sedan 4 door, we love it. Pile the kids and fishing poles and kites and lunch boxes and ,,, and ,,, and into the trunk and go out for a fun day.
Have FUN with your project.