just a couple of questions

So...the nitrification process is the same with fresh as with marine, right? I am not in any hurry what so ever to do anything, mind you, but if I added the correct amount of salt to get my density etc. would the bio in my tank continue to live?

Similar, but freshwater and marine bacteria are different. If you have a fairly salty brackish tank, you might be able to just slowly up the salt content and get saltwater-tolerant bacteria colonies, but simply running the cycle for the tank will probably work better than trying to keep freshwater bacteria colonies for nitrification.

I know there is some debate about keeping substrate in "Berlin" tanks.

And the debate rages on, apparently... Some people say that their deep sand beds 'crashed' and they lost their entire tank. This supposedly happened because their tanks got too old. The truth is that there isn't much evidence besides anecdotal as to what is going on, but deep sand bed is still considered the best way to go for anyone pretty new to marine aquariums, because it basically absorbs some mistakes that newbies make. Every year or so, replace part of the sand, if you are concerned about a deep sand bed crash. This forum is quite pro-deep sand.

I have a good deal of crushed coral now, should I keep it, thin it out and add live sand to it, or say adios all together?

That's really your call, because it depends on what type of tank you want. The particle size on crushed coral tends to be large enough that it is very good at trapping and hiding away uneaten bits of food, etc. This can lead to a nitrate problem down the road. You can certainly do something like a 75% sand, 25% cc mixture to make a deep sand bed, though. In fact, jawfish would love that mixture.

I also have quite a bit of tufa rock. I have been told I could use it as base and add live rock to it to colonize the tufa rock with the coraline algaes?

Tufa is pretty much the best of the base rocks. You can add any clean, porous rock to your tanks and they will become live rock with time. Tufa is so good because it is porous, but it rarely leaches any chemicals into the water like many volcanic rocks.

Would adding a good skimmer with the sump be enough filtration?
I have always been a believer of never enough filtration, soo, I have seen most everything out there, besides the sump, skimmer, LR, even the canister too if I want, along with some power-heads to move things about, am I missing anything?

With 1.5 - 2 lbs of live rock per gallon, a skimmer and pumps or powerheads should provide all the filtration you need, if you can keep a 'cleaning crew'. You cleaning crew is mostly marine snails and hermit crabs that devour leftover food, waste, and some excess algae. You want your tank to have enogh pumping power that the total gallons per hour is at least ten times the number of gallons in your tank. Getting a current that is unstable with eddies and such is also beneficial.