Sekai 2000 tire and rim? I have a Sekai 2000 bike and the rims are bent very minutely. If I turn the wheels front or back and put my fingernail in a fixed position close to the rim, it is less then 1mm. Is that anything I need to worry about? I will be riding out in the country on asphalt and then down a gravel lane. 

I am considering replacing the rims and tires. I kinda of want yellow tires and rim since the bike is blue. All the running gear is brand new and some brand I cant recall at the moment. I know the tires are 27x1 1/4 or 630 x 28. Do they have yellow colored rims for that size? I know the rims aren't that important but I like to admire the little things. either that or black or white rims that will contrast between the blue and yellow.
Some general advice:

The bend/wobble is likely nothing to worry about and you can search this site or Google for how to true a wheel. If there's less than 1mm of un-true-ness, I wouldn't even worry about truing it. 

A new wheelset will likely cost more than the bike, and since it sounds like you have a perfectly good one on the bike already it's hard to recommend doing. That said, if you want colored rims and tires, you're likely going to have to perform a 700c conversion to take a modern wheel since hooligan colored stuff wasn't reasonably common on road bikes in the pre-1980s as far as I can tell (and 700c became popular after that). The 700c conversion essentially requires the ability to move the brakes down about 4 mm and spreading the frame (cold setting it) to fit a modern hub. Then you can buy some (generally low quality) 700c wheels which are colored to your liking, along with tires provided they clear your frame (you're going to have to measure it). 

As for handlebars, note that changing the handlebars may change your fit. Make sure the bar has the right diameter for the levers to clamp to as well as your stem. 

There are a lot of fenders on the market, so go find something you like - make sure you have the eyelets or mounting method for the fenders you choose.