Dead Shepheard: Invoking Christopher Marlowe who died in 1593. Marlowe's "Hero and Leander" contains the line "Who ever lov'd that lov'd not at first sight". He is also the author of a popular lyric "the Passionate Shepherd to his Love".

neighbourly: "Love thy neighbor as thyself" (Leviticus 19:18)

covetousnesse: would be greedy: "Thou shalt not covet thy neighbours house, thou shalt not covet thy neighbours wife, nor his man servant, nor his maid servant, nor his oxe, nor anything that is thy neighbours" (Exodus 20:17)

ere-while: a little time ago

peevish: silly, perverse

parcells: separate parts, items

what had he to doe: what cause had he

remembred: remind myself 

all one: doesn't matter

omittance is no quittance: failure to rebuke him does not mean that I pardoned him (quittance = legal release from debt).

tanting: taunting (pronounced as taunting); Phebe is tanting (high and mighty, stuck-up), so she will tant (answer back in equivalent terms) Ganymede in hopes that he will find her letter tanting (sexually stimulating).

strait: immediately

passing short: exceedingly curt