I have done basically what you are talking about on my 73 Cuda and will be doing it again on my 70 RR. I could not find any modern replacement that offered bulk head connectors similar to the original, rather all of the aftermarket harnesses have hard wired harnesses meaning that all of the wires are connected to the fuse block. On my Cuda I did make a variety of disconnects so that I could connect various circuits but not the engine harness and front end harnesses. I thought about it and could have used multi pin connectors to do it, but in the end it just didn't seem like it was worth it. I might try this on the RR when I get to that point.
A few points on wiring and going the route of installing a new modern harness; you really need to spend a lot of time thinking it through, making a variety of wiring diagrams that include all of the components you want to use or think you might want to use. This way you can configure the harness before you install it all into the car.
As to mounting, again you are not going to find a direct replacement to bolt/screw into the same location as the original; you would have to either close up the original hole or make a place of some sort to cover it. I always hated where the fuse block was mounted so on my Cuda I mounted the fuse block in the glove box (which I remade out of metal). Makes it very convenient to inspect and replace fuses. I removed the entire dash, mounted the fuse block, and ran all of the wiring before reinstalling the dash, made it SO much easier than trying to do it in the car.
There are some really cool electrical block solutions out there, but they all come with a price. I would love to install an ISIS Electrical system but they are just so expensive. The great thing with all of the modern systems is that the wires are marked as to their function every 6" so running them is relatively easy. There are a lot of good systems out there, I have used Kwik and EZ systems which were fine. I would not pay the money for a Painless because, well they are not painless and you are spending money you don't have to due to the name. Ron Francis is good as well. There are some guys who make their own which isn't as difficult as it would seem but a lot of work.
Going modern means you are going to have to deal with connectors, the originals on vintage Mopars were Packard 56 however there are many others to include Deutsch, Metri Pack, weather pack, etc. and they all have different connection/assembly requirements so you will need some tools and an unedrstanding of each that you will want to use. There is some over lap in terms of tools and each has its own nuances as to where/how to use them. Generally, I stick to Packard 56 connectors for high amp uses, metri or weather pack for anything that might be exposed to weather/water.
Hope this is helpful.
