Bella every one's perception is different so don't just take my word for it, but that doesn't sound correct. Any way you can post a picture? It shouldn't have a yeasty smell and definitely shouldn't look like risen bread. But take it from me and others on here you've made it this far don't ever throw a cheese away by looks alone. Nothing in it, unless your raw milk was tainted from the cow, will hurt you and it may turn out to be the best tasting cheese ever. Just age it no matter what eat it and decide from there, but I'm not saying this about your cheese. I would have to see some pictures to make a better call.
As for smoothing out, it's one of those human learning things. At first you will knock curds loose from the edge and pull some up out of the wheel, but by the time you get to your second Stilton it will start to work better. This applies to the handling of the cheese too at first I was timid to handle it as it was so fragile but after your mind and body learn from handling it, it will go much easier.
Here is my procedure. I slide the cheese from the mold, my mold releases cheeses easy since the cheese is still wet it slides right out. I leave the follower on as way to move the cheese without damaging it by holding it. My follower has embossing on it and suctions itself to the cheese you follower may or may not, more than likely it will hold, just be careful so it doesn't slide off of the follower. I then use the follower as a plate and take a glass of warm/hot water and a large spoon. I dip the spoon in and rub the top, basically what I'm doing is dissolving the cheese with the wet and slight heat, not melting so I wouldn't use super hot water (plus the hot water might kill the Blue Mold). I use the edge of the spoon to burnish with a little water the edge of the cheese on the top, I work from the outside in. If you work the reverse you'll break the edge. You'll know when you need more water which is about every few seconds, not a ton of water but it needs to be slick, too much water won't hurt anything, it's better than too dry. When it gets too dry the cheese will stick to the spoon and you'll start to pull curds from the wheel. DON'T be afraid to touch the cheese, if a curd pulls loose push it back with a wet spoon or push it in with your fingers. Since you are basically dissolving the cheese surface and using it as Spackle to fill in the holes and cracks it will make the surface slightly uneven, there is no way around this but doesn't look bad.
So I start on the top and then work on the sides. The sides because they have been against a mold are a little more solid and you'll have to use more water to start the dissolving process, but just work your way around like you are decorating a cake.
When the sides and top are done I take a bamboo (sushi mat) mat and place in on top of the cheese. On that I stick a piece of plastic made out of cutting board material, Tap Plastics or any plastic place will sell it, make sure it's either cutting board material or food safe or a piece of wood. Make sure it's slightly bigger than the cheese. So place that on the mat and flip the cheese. Hold tight so it doesn't slip when flipping. Next pull off the follower and work on the top, now you're done. If you do buy or make the plastic board get a couple. I always have my cheese sitting on a bamboo mat and board or else when you go to flip the bamboo will fold up and crush the edges of the wheel.