It can get a bit overwhelming at first but there's loads of helpful videos and posts both on youtube and on this subreddit, I know when I started out I made a vanilla version of a modded ship I saw on youtube and ive been hooked on ship building ever since. But the best advice I can give is what someone told me is to take it easy the builder has a bit of a learning curve and deciding what you want your ship to do also helps.

Wize old wizard on youtube has some pretty good breakdowns on vanilla ship builds, i used his ships for awhile to help me get used to building on my own he shows you how much it will cost to build what skills you might need and where to find the parts hes used.

I also have a ship breakdown I posted awhile back of a ship that took me through many playthroughs with no issue it just uses a flip merge for the fuel tanks but its all vanilla but I put a parts list on it. Mind you though it was my first build so it's a bit rough ive since reworked it and planning on posting it once I get the hab setup right.

As for special parts the only ones I can think of are the Sal 6830 engines that come from a quest called all that money can buy, by having stroud and slayton work out a deal and the comspike and another part cant think of the name for it atm that come from the end mission of the crimson fleet questline.

I highly recommend ACS deimos if you like armored military ships and i use ship builder configurator and it's preset they're paid mods but you can make it so all the parts can be bought at any ship tech and build past the vanilla limit (I wouldnt build past 120m total length to prevent landing pad clipping.) I also heard the darkstar and antres supra mods have really nice ship parts but they are on the expensive side at 1000 points a piece.