I don't see a lot of reason to replace the Topeak rack unless you have some reason why it's bad. To an extent, ditto on the Topeak trunk bag. We're a car free household, and we've got a trailer, 3 panniers, a messenger bag, a couple backpacks, various small bags, a couple seat bags and a bike basket. If you get around a lot on a bike, chances are you'll gradually end up with a lot of ways to carry stuff. The lack of trunk bags is not coz they're bad or useless, but more because I like baskets. For panniers, I don't think it really matters a lot which exact ones you buy. For grocery and around town use, I really like to have 40L. There are a lot of 40L pannier options that are sturdy, fairly lightweight, and will hold up well to touring use as well as daily in town use. (personally, I bought mine from REI on a steep discount)

For a light, consider grabbing a camping headlamp rather than just replacing your Planet Bike light. $20 will pick up a reasonably light and small headlamp that's also bright enough to be useful. My partner uses a combo like that and is very pleased with it. It's not as bright as my generator powered Lumoteq but it works and is quite cheap.

Some bike shops will let you do test rides with your panniers and even loaded test rides. If your local Surly shop is like that, I'd probably buy from them, whether you end up on a Surly or not.