Skittish/Jumpy Cat: How To Make More Confident and Content?

My poor cat Sunny is still taking a long time to recover from having another cat in the house that she didn't like. While the other cat was in the house there was quite a pee-off and marking spree. The other cat is now gone and she's been by herself for two three months now. Shes been much less accident prone from what I can tell but I still think she still marks in certain places and I have been realizing they had peed in a lot more places that previously thought. I've been cleaning as best I can. So far no obvious huge markings or daring to do it while I'm watching though and her litter box is now being used much more frequently for pee.

The other cat is long gone but Sunny is still very cautious as if she's still there regarding entering rooms or trying to get off of a bed (as if the other may jump out at her from under the bed). We had kept them separate for the most part and most times we did try to get them to socialize the one did chase her.

She's otherwise a very fun and friendly cat who loves to stick around you (not 100% a lap cat) so she's not a total bolt-er, she'll greet me when I come home follow around for pets just fine and loves when company is over she'll sit with them to get scratches. She does enjoy going outside (I've realized some of her complaining was wanting to go outside,  this makes her happy so I'm slowly allowing small windows of outside time to the backyard) but her skiddishness and nervousness (she was overgrooming her rear too) and being very smell driven (constantly sniffing things, more so than any cat I've had) is making it a bit hard to observe her and it feels like she's not 100%. She consistently will get very cautious over things lying on the floor that weren't there before (coat hanger, a sock) and she seems to struggle realizing where her food bowls are or if it's okay to approach them sometimes when I put dinner in them (not always but I usually have to adjust her). I'm not sure where this behavior comes from. I'm pretty sure she has okay vision too. 

I'm trying hard to make her happy otherwise, I got her a cat tree which she ignored but I moved it to another spot in the room and now she loves the enclosed box/lounge part, she has lots of mouse and lizard toys but seems to enjoy feather-dancer type toys the best but isn't always 100% into that play either or we never play terribly long. I'm struggling to figure out what other kind of toys she'd like? I'd love more enrichment but I can't think of much that she doesn't show interest in. Not impressed by laser pointers. She loves her KONG scratching pads a lot.

Any idea how I can we make her a bit less scent driven? I've tried the feliway handheld spray on things but that's so expensive for just a little thing. I have her on a calming collar on her, feliway plugged in her room, I try to medicate with Prozac but she's a horrible medicine taker. I bought the calming drops to rub on her ears too. Should I keep pilling her?

Any additional suggestions? I feel like she's improving but some of her skittishness is so silly and seeing her jump all the time when there's no need makes me sad she cant relax.

Catnip?! It seems counterintuitive, but we found it's worked the best with our over anxious cat. We also tried kitty Prozac, and then camomile drops in her water. I would keep the floor clear of laundry, especially since you're trying to fix spraying ... She may try to make it less scary by marking it.

She really does love catnip! She loves a particular spot in the carpet in her room where we put a lot of it actually. Should I sprinkle it everywhere?

I wouldn't sprinkle it everywhere - sounds messy - but maybe put down fresh nip more often, and really take advantage of those kitty highs to engage her in play.