Tho hops in the bottom of the carboy will not kill the beer but is not needed. So once you get comfortable with the process it's a tweak yo can do to improve your beer another tiny bit.
Just get a strainer and when you are pouring your wort into the carboy have it pass over the strainer. It's not ultra crucial but it's a good thing to do.
clumps of doughy looking things
Again - maybe not NORMAL but all sorts of odd things happen so no worries.
Boil the water, add the sugar - let cool. dump in bottom of bucket and when you siphon into the bucket it will all blend together . . in theory. another wonder of nature LOL