First off, I'd say that what you're experiencing is pretty normal...especially for a boy. My son was also in a Montessori-type program until kinder...and about half way through kinder he went through a period where he had the same problems finishing his work...and then again in first grade...and then again this year in second grade (we're just coming out if it now...thank God!!!).
In every case, I worried and wracked my brain trying to figure out what to do...and so did his teachers. ...and now that we're on our third round of this "game", I'm convinced that none of the things we tried are what actually caused him to start doing his work again...that these episodes were nothing more and nothing less than his attempt to control his environment. ...and once he collected enough evidence to know that his behavior wasn't leading to desirable outcomes, he tried another strategy. Specifically, such episodes are almost always followed by a period when he goes out of his way to impress others (me, his teachers) with his ability to do the work...and when he gets rewarded for doing so, the behavior continues until the next bid for independence!!!
That's really how his teacher and I pulled him out of his most recent troubles finishing his work...this one lasted for nearly six weeks, but once we started specifically giving him rewards (attention, stickers, special privileges, etc...) when he DID complete his work (while simultaneously deemphasizing his failures rather than making a big issue of them), it took less than a week for him to start finishing ALL his work on time so he could earn more of those rewards!
See if you can get his teachers to cooperate with you in temporarily exaggerating the positive attention/rewards he gets when he does finish his work on time...even if it is only one assignment out of half a dozen or more on a given day, make a HUGE deal out of the positive and try to minimize the negative until he starts finishing more than half of his work on time. Only then can you go back to using negative reinforcement (e.g., isolation) to motivate him to do all of it. Just make sure that he is always getting more positive than negative reinforcement! If you don't, he's much more likely to start believing that he's just "a bad kid" who "can't" (rather than won't) do his work. My son was at that point this year before we figured out what was happening...the increasing amount of negative reinforcement he was getting had nearly convinced him that he wasn't capable of behaving and doing the work...but once we (his teacher and I) realized what was happening and started actively seeking opportunities to praise and reward him for doing what he was perfectly capable of doing, his confidence increased. ...and last week, he brought home straight As on ALL of his school work for the week!
...and one final thing to remember...something my son's kinder teacher pointed out when he first started having problems in her class...that Montessori students often have problems adapting to the structure (timetable, rules, etc...) of a regular classroom compared to the students that came out of a more traditional preschool experience...HOWEVER, the Montessori students often caught and surpassed the kids from the traditional classes by the end of the year because they had far superior critical thinking skills! The school he attended had a Montessori AND a regular pre-k program so she had been observing this phenomenon for more than 20 years...and she was right about my son. It took him until the middle of the year to adapt to the structure...but once he did, he quickly caught up and entered first grade testing at the second grade or higher level in everything except reading (and he jumped nearly three grade levels in reading during first grade...again, after he adapted to the structure of yet another new learning environment!).