Even though the gunner update has added some very powerful new weapons, I want to stick with swords and bombs as a backup in case they get nerfed. I'm currently going for the Blackened Crest (and then the Crest of Almire) as a shield and am still narrowing down which bomb to get (A damage-focused bomb with some kind of lasting AoE attack.).
In the meantime I need to craft a better four-star sword, armor, and helmet. I'm lost here. I've got no idea what to get aside from the fact that normal damage/protection isn't viable on its own in the long term.
The answer to the question "What 4-star items should I get?" is "Whichever ones lead to the 5-star items that you want." You want to plan in terms of 5-star items, because that's where everything ends up. You don't want to get trapped in an alchemy tree that doesn't go anywhere (such as Winmillion).
My detailed sword guide is written for people in your situation. It covers basic concepts, choosing swords, choosing guns and bombs to go with swords, choosing armor to go with swords, etc. Maybe it will help.
To address your specific questions, we need to know:
* What are your immediate goals? To complete the rank missions?
* How many weapon slots do you use? 2? 3? 4? With how many swords, how many guns, how many bombs?
* Are you feeling adventurous? Are you a skilled player, playing on a strong Internet connection and computer? Do you like taking risks? Or do you want to be a little more careful than that?