It's way too big a subject to offer much advice, so this is general rather than specific - Play around with it and when you find what works for you, go buy the best quality of that type. This has worked for me, I've ended up with very little cycling gear, but it all suits me perfectly, none of it will be replaced till it wears out, which in some cases will be never. My favourite makes are - Showers Pass, Rohan, Howies and Vulpine, some of it looks eye wateringly expensive, but a £70 shirt that you wear 15 weeks a year for more than ten years is better value than one that keeps getting replaced.
I stopped using SPD's last year after an accident left it painful to twist out of them, after using them for the last twenty years on every ride I'm surprised how much I miss them - not at all. I'm still playing around with shoe and pedal combinations, but they're all OK and I can't see my going back to SPD's. I'm not saying what's right or wrong, but sometimes we do things because everyone else does and then discover there was no advantage...
Saddles, yes I know it's personal, I'm a convert to Brooks C17's, I'm gradually moving the whole fleet onto them, saddles I thought were OK seem a lot less comfortable after riding a C17.
Padded shorts - again it's personal, I do most of my riding in non padded underwear, but most of that will be on and off the bike, maybe all day, maybe 60-80 miles, but rarely an hour in the saddle without a break. When I have longer days with few breaks, I use padded bibs, Howies and Vulpine. I might be OK on some of these rides without padding, but by the time I'll discover that's a mistake it'll be too late. I also have some padded underwear with much thinner padding than shorts, they're OK but the riding I used to use them for is fine without on a C17.