So.. I'm using D'Addario Nickel Wound .45-.100 strings and for me, they're too bright and too... "flimsy" I guess you could say.

When I play, I usually pluck or play the string pretty hard especially during the build up or the chorus of the song. It may have to do with the action of my bass, but when I do play hard, the strings hit the fretboard (i'm pretty sure it's the fretboard) and make a clack sound.

If it is the strings, do you recommend a more darker toned and thicker gauge string set? I usually play from Drop C to Standard tuning if that helps.
Hmm, I mostly play in standard while performing. The drop C and D is usually for just at home or playing with friends.
Try a slightly heavier gauge and a setup, but when you downtune from that they are going to get loose.

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DR's are it! Get the DDT's. I just started using them and they're one of the best I've tried or drop tuning. I'm using12-60's or drop tuning they're outstanding. I put them on and,no joke, they went right in tune. I didnt even have to break them in and they held in tune for a long time right out the box.

They feel and sound awesome. Super stable. Not gonna use anything else on my Drop tuned axe!
And if u try to get remotely close to standard tuning with the ddts, you will completely mess up your bass's neck. I guess for standard tuning only a slightly heavier gauge will do. Maybe like 50-55 ish.