You can actually use the stain as a way to find the flaws you want to work on. It's also easy to find the sanding marks you missed. Stain it a dark color and then sand it down again....... Doing this will bring the grain out to your sight much better. You can do this several times if you like and each time you'll see the grain better.
As to the piece that is missing, if it's the one I see on the top of shank, I wouldn't even worry about it as it will still look good in a smooth finish. I've rusticated pipes and while I like the look when done right, I prefer seeing the grain of a smooth.
The shape looks good and if you like it, that's what matters.
You can bend the stem in several ways. But for safety (So as not to close the airway any) I insert as many pipe cleaners as I can safely do into the airway before bending. You can use a candle or a lighter to heat the stem for bending, but be careful, as you can easily overheat the acrylic, causing the outside to sink into the airway, leaving a divot on the outside of the stem. I've just recently started using a heat gun with adjustable heat settings and find this way much safer for heating and bending the stem. Also remember when bending the stem, bend it only enough to make it comfortable to light and smoke when in your kisser. I've seen many pipes with too much bend in the stem, and while the amount of bend looked like it fit the pipe better, made it more uncomfortable to light and smoke as the bowl then cants forward too much for my liking.
Also wanted to say, that you need to be careful when heating and bending the stem so that you don't get any bend in the tenon...... That will throw the line of stem and shank off. I bend my stems going just a little at a time, then insert them back into the pipe several times to test fit the bend. It's easier to bend a little at a time and get it just right than to overbend it then try to reverse it.