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Merrington was Lee's first choice for assistant manager but the deal collapsed after a combination of salary and contract-length expectations led the coach to reject The Lions' offer.
"Dave could have played a vital role in what I'm trying to do here," reflected Lee, who also failed to pursuade former Fulham coach Paul Bracewell to join his staff at The Den.
"He is a magnificent motivator of players, and brought through Alan Shearer, Matt Le Tissier and the Wallace brothers at Southampton.
"But there is a cut-off point in terms of finances, so unfortunately we now have to go and look elsewhere.
"The acting chairman (Theo Paphitis) tried to make it work, so I'm not criticising Millwall - but I can also see Dave's position."