I've been down this road a few times.
The original suspension on your 48 Plymouth was very modern at its time. it was well engineered and works well with only a couple modifications.
There are several places that sell Disc brake conversions for these cars, including Butches, Fatman, Sacarbird, and Rusty Hope to name a few. My preference is towards www.rustyhope.com.
The second place that needs modification is the upper shock mounts, originally The shocks mounted between the upper control arm and the lower control arm. Made for a nice soft cushy ride, but was a bit lame in the performance area. The fix is to relocate the upper shock mount to the frame. Again, there are several places that offer a "kit", or you can make your own.
Another thing that has been done is the installation of a rack & pinion steering in place of the original steering box. There are also a couple different methods this has been done, and I believe there are "kit" out there for this too.
I have a 48 Plymouth business coupe sitting on a complete Dakota frame and can tell you it is a major project. I have it on the road now, and its a blast to drive, but not something for a beginner. There is a build thread here in the street rod section, look for it.
That said, a Dakota clip matches up with the original frame at about the firewall, where the Dakota slips right in like it was designed to do so. As a whole, frame clips are a pita because you have to figure out rad and front sheet metal mounting.

When your ready to install your 360, it fits real nice if you off set it about an inch and a half towards the passenger side. Be sure to keep the drive train straight, side to side, everything should still clear, but you may need to modify the passenger side firewall, just a bit, with a bfh to clear the valve cover. You will also want to update the rear axle. The track width of your Plymouth is in the 61" wide area, a wide selection of modern rear ends fit well, like the disc brake Explorers.

I think I would pass on the Van master cylinder, (might not be a bad thing to bag and shelf though) I think it will want to occupy the same space as the motor will. I have a Dakota booster and master on my coupe, and have used Dodge truck and Volare masters and boosters before.

We built a 47 Plymouth club coupe for my son with a 360, 727, 8 3/4 with 3:55 gears. We did the disc brake conversion with a Volare master and 11" drums on the back. when you did a panic stop, you looked in the rear view to see if the guy behind you could stop, that thing would have out braked anything I had before or since. I don't think we ever got around to the upper shock mount relocation. That car was a lot of fun.

Picture is my current 48 business coupe on a Dakota frame.Gene