There should be a comma after hair, a comma after Pern, and a comma after most. It should read "than", not "then". "Like most people on Pern" is an explanatory insertion that the sentence could rationally do without, meaning it must be bracketed by commas. Further, "his is longer than most" is a complete thought joined to another complete thought ("He also has dark hair") by a conjunction ("though"), so it must be separated by a comma. Here, that comma combines with one of the two bracketing "like most people on Pern". "Being nearly halfway down his back" is also an explanatory insertion that the sentence could rationally do without, meaning that it, too, should be bracketed by commas. Because it comes at the end of the sentence, the second comma is displaced by the period, so it must only be preceded by one. "Then" is a time reference, used to indicate a sequence of events. "Than" is a comparative conjunction joining "his [hair]" to "most [peoples' hair]".
There should be a comma after "however". However is a modifying insertion that the sentence could reasonably do without. There should also be a comma after "blind)", because "as well as fair skin" is a listing modifier.
"Lean" and "muscular" are adjectives modifying the same noun (frame), and should be separated by a comma.
There should be a comma after "blind", because "Seeing as he's blind" is a modifier for the rest of the sentence that could logically be done without. If he's blind and doesn't pay much attention to his wardrobe, how does he have a preference for colours he can't see?
There should be a comma after "matches". This is an if-then statement, which means that there should be a comma here, because all if-then statements contain two complete concepts. If <concept>, then <concept>. If Conysk says it matches, then he's good to go.
There should be a comma after "protection" for the same reasons as in the previous sentence - these are two complete concepts joined by a conjunction.
There should be a comma after "spoken". "Quite and soft spoken" is an insertion which modifies the sentence but could rationally be done without.
There should be a comma after "handicap". These are two complete concepts joined by a conjunction.
"More often than not" is an insertion to the sentence which could logically be done without and should be bracketed by commas. Further, this is another instance where the word choice should be "than", not "then". Here, you are comparing "often" and "not".
"Hold" should be capitalized. "To be quite honest" and "either" should both be bracketed in commas.
There should be a comma after "however".
"Grounds" should be the end of the first sentence. The second section of this should be a separate sentence. There should be a comma after "locked". Otherwise, it sounds as if he only cannot stand it if it's locked due to a prank, but as though it's fine if it's locked for any other reason.
There should be a comma after "door".
This should be entirely in third person. Please remove the word "you".
There should be a comma after "boy", because "with one difference" is a modifier to the rest of the sentence. The ellipses should be replaced with a colon.
There should be a comma after "yes". There should be a comma after "blind". Why would he gain amazing reflexes? Reflexes are a cultivated thing and, even when inborn, are not inherently tied to the presence or absence of sight in any way. If you want him to have amazing reflexes, you can make it an inborn trait, but don't try to tie it into his blindness. It should read "heightened senses of", rather than "a heightened sense of", because you're tying the phrase to two distinct senses.
There should be a comma after "however". I also question your word-choice with "however". You just provided several examples of how his body overcame his handicap, then implied that his handicap should have slowed him down. This is contradictory. Perhaps you should replace "however" with something like, "thanks to this", "as a consequence", or "fortunately, this meant that".
"Sadly" and "though" should both be followed by commas.
"Harper" should be capitalized. It is a proper name.
"Years" should be "turns". There should be a comma after "later". There should be a comma after "apprentice". "Three turns later" is a modifying insertion that the sentence could logically do without. "He was a senior apprentice" and "his mother asked him to stand at a wher clutch" are both complete thoughts and should be separated by a comma and conjunction.
"Hold" should be capitalized. There should be a comma after "handlers", because "the hold needed more handlers" and "Conyr agreed" are both complete concepts separated by a conjunction.
"Brown" should be lower-cased.
There should be a comma after "team". This sentence contains two complete concepts joined by a conjunction at this point. The name "Cosk" does not reflect a deep bond such as you indicate here, but rather, a generally shallow one. The deeper the bond, the more of Conyr's name the wher should take. To reflect the bond you indicate, his name should have been "Conyrsk". This is another instance where you use "then" when you should use "than". Please adjust this and look out for it in future writings.
"Years" should be "turns". "Threw" is a verb, past tense of "throw". The word you're looking for is "through".
Why were there so many wild wher attacks? Wher populations tend to be carefully controlled for just that reason.
There should be a comma after "bronze)", because this end section is an explanatory insertion that the sentence could logically do without.
There should be a comma after "brown" because these are two complete, coherent concepts.
There should be a comma after "however" and a comma after "quietly". "In the end" should be bracketed by commas. There should be a comma after "killed". "Hold" should be capitalized, and there should be a comma after it. If you have any questions about the rationale behind these commas, please let me know.
There should be commas after "after" and "stand".
There should be a comma after "did", commas bracketing "in no less words", and a comma after "gone". I don't understand what you mean by "in no less words". How did a newborn know about Cosk?
"Threw" should be "through". There should be a comma after "training", there should be a comma after "Cosk's", and there should be a comma after "adjusted".
There should be a comma after "ago". There should be a comma after "handlers".
There should be a comma after "light".
There should be a comma after the first instance of "rank". The second instance is unnecessary and should be removed.
There should be a comma after "side". "Then" should be "than". The "do" is unnecessary, though this is not actually wrong and does not have to be changed.
"Then" should be "than". There should be a comma after "golds".
The word "you" is second person. Personality should be in third. Please rectify this. These two sentences contradict one another. "She isn't the most forgiving creature" implies that she forgives, but not easily. The second sentence outright declares that she does not forgive anyone but Conyr, and him, only rarely. There should be a comma after "hers".
Wickedly smart and a good problem solver, for a wher, implies the intellect of about a five year old. This is not a problem. I simply want to clarify the point.
There should be a comma after "Conyr". This is another instance of the "you" problem.
"Though" should be bracketed in commas. The word "you" is present, again.
The words "as well" should be bracketed by commas.
As a final note, the biggest problem with this application is that it presents a lack of understanding about the process by which whers impress. Please take a moment to review our guide to
how hatchings work, specifically the section on whers, and our informational thread
about the whers of Pern. These will help clear up the problems in Conyr's history for you.