Yes the brakes will be an issue if you go 26 inch. Don't do it. There's no fix (or at least nothing easy or cheap) for that sort of mod.

29'er and 700c rims are the same size diameter wise. The 29'er rims tend to be wider since they are intended for use with fatter tires. A lot of 700c rims are intended for racing or near racing sized tires. Check the rim width spec to figure out what you want.

For a touring setup you probably want to use a 28mm or wider tire. For that size the 29'er rims that are intended for the speedier 29'er riding will be the right width for the 28 to 34mm tires quite easily.

If you look up "cyclocross" or "touring" under wheelsets on most stores and on ebay you'll get back a lot of good options. I recently got a set of modern LX centerloc disc ready hubs laced to touring style rims that were labeled as touring/29er by the ebay seller. Lacing was 14ga straight guage spokes. So nothing fancy but nice and solid quality stuff. Price was $160. I'm sure you can get a similar deal from most online stores.

Although I've built up around 10 sets of my own wheels over the years I find that I can't buy the parts for what I can buy premade wheels for. I'd love to use butted spokes but again teh price is going up on those as well. And the other big issue with machine built wheels at this price point is the spoke tension. For the price they are a heck of a deal and if I need to watch them for signs of settling in and re-tension them then that's OK. Although I'm sure most sets will be just fine for a long time.

My new wheels are going onto a new bike as well. But I went a touch more posh with a Soma Double Cross frameset.