Welcome Ethan.
I'd add the 390 jug, advance the timing and leave your muff modded. I wouldn't touch the ports on it without the proper tools. It's very easy to ruin a jug and chances are that you'd do more harm than good.
The issue with clamshell motors is the amount of work needed to modify them. It's very difficult to check port heights because you need to put the entire engine back together and take it apart everytime you make a change. Also, adjusting the squish is nearly impossible to do unless you have some special tools and series skills. There are software programs around that can help you measure ports and not need to use a degree wheel.
If you choose to play with the ports, make sure you've got some diamond coated balls to chamfer/debur the port edges.
Good luck bud, and remember, one of the bar studs needs to be removed (and generally sacrificed) to pull the engine out.