1. He was already a two weeks into his fifth year... – why a two weeks?
2. Oh, I'm sorry Harry... – Oh, I'm sorry, Harry... – an addressed person's name is always paranthetical and should be set off by commas.
3. The least she could do is join me for Saturday breakfast. Harry thought... – The least she could do is join me for Saturday breakfast, Harry thought... – quoted speach should be set off by commas.
4. Okay then... - Okay, then...
5. "Come on Ron, its Saturday," Harry replied, sensing that something was off, "Ready to go to Hogsmeade?" – "Come on, Ron, it's Saturday," Harry replied, sensing that something was off. "Ready to go to Hogsmeade?" (It's = it is)
6. "Sorry, Harry, I feel awful." Ron said with a slight drawl. – "Sorry, Harry, I feel awful," Ron said with a slight drawl.
7. "Ah, must have caught flu then?" Harry replied with worry, already he could see his Hogsmeade visit coming to an abrupt end. – "Ah, must have caught flu, then?" Harry replied with worry; already he could see his Hogsmeade visit coming to an abrupt end.
8. "Here are some bangers and scones," Harry replied hopefully, "See if this helps..." – "Here are some bangers and scones," Harry replied hopefully. "See if this helps..."
9. "Oh, I feel dizzy!" Replied Ron... – "Oh, I feel dizzy!" replied Ron...
10. Hermione glared at Harry which caused him to feel guilty, even Harry had to admit to himself that she had a point. – Hermione glared at Harry, which caused him to feel guilty; even Harry had to admit to himself that she had a point.
11. Harry if you could get me... – Harry, if you could get me...
12. You are going to Madame Pomfrey, you never know, what if it's something poisonous you ate? – You are going to Madame Pomfrey. You never know, what if it's something poisonous you ate?
13. ...it had been awhile since he asked... – ... it had been a while since he asked...
14. "We were going as well," Dean replied with a grin, "Why don't we all go." – "We were going as well," Dean replied with a grin. "Why don't we all go.(?)"
You should really do something about your punctuation... For an HP fanfiction writer, it's a good idea to read throug all the threads here: http://www.fictionalley.org/fictionalleypark/forums/forumdisplay.php?s=&forumid=141
Don't think bad of me. I just wanted to test my grammar skills ;) | 
