Clifford - who won the Conference title with the Pilgrims in 2002 and later went on to own Ilkeston Town, another of the sides he represented - has taken on the role as part of a reshuffle at the Northern Premier League outfit.
“I’m really looking forward to the challenge ahead," Clifford said.
"We have an excellent group that needs to kick on if we have any aspirations in pushing towards the play-off spots.
“We all share the same vision and aspirations and I’m looking forward to working towards those.
“I’d like to thank the chairman (Chris Munroe) and the senior management team for this opportunity."
Former boss Steve Chettle - the father of one-time Boston loanee Callum - has moved upstairs to take on the director of football role at Greenwich Avenue.
Clifford will be assisted by Liam Hearn (player-assistant) and Wayne Scott (coach).
"I’m excited that in Steve, we have a great figurehead that will add value to the management team,” Clifford added.
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