There's a lot of info in the HAMB archives. I'm getting ready to hop up a '53 331 as well.
Everyone says that breathing is a problem on the 331 that only '62 and earlier 390 heads can fix. If you go with a solid lifter cam instead of the hydraulic cam you can use Studebaker adjustable rockers on the Caddy rocker shaft. I think Howard's still regrinds cams and Isky cams are sold on eBay.
Also, the block can be bored out quite a bit, there is a lot of wall thickness to work with. 1/8" over to the 4" 390 bore is a cinch. I was thinking of putting a 390 crank in mine, but the bearing journal widths and diameters are different so a lot of crank grinding would be necessary. I've heard that it has been done but I have yet to get in contact with someone who has actually done it.
Here is a good article on rebuilding a 390 for reference: http://hotrodcaddy.com/?p=139
Sounds like moving to stiffer valve springs and a new cam are a must for performance.
Lots of intake manifold choices from stock 390 4-barrel and 3x2 stuff to aftermarket. Check the HAMB and eBay.
The later timing covers have a rubber crank seal instead of the rope seal. There is also a mod to use a Chrysler rear main seal with some shim stock to replace the rope seal there as well.
Is you car pretty much stock otherwise with an automatic transmission?