I think the combination is
Under net, counter and employ longest leg (10)
HYPOTENUSE (HYPO + NET< + USE)
Sports captains often realize even beginners get points (5)
SCORE (initial letters)
Oddly swindled by façade (4)
SIDE (odd-numbered letters of SWINDLED)
Number of bakers sleep before noon? (5)
DOZEN (DOZE N)
Mess up plants without energy of Motown singer (7)
MARVIN'S (MAR VIN(-e)S; Marvin Gaye); this is the punctuated one mentioned in the preamble.
Fantastic comic publisher associated with British universities (9)
MARVELOUS (MARVEL + OUS, presumably referring to the Open University or maybe Oxford University)
Poor chance: I am large and robotic! (10)
MECHANICAL ((CHANCE I AM L)*)
Gallery shows inspiration against hesitation (6)
MUSEUM (MUSE UM)
Nearly cooked salmon with bit of thyme instead of pinch of nutmeg (6)
ALMOST ((SALMON with T instead of N)*)
Endlessly want class (4)
Showing love, romantics are a thing of the past (4)
Quiet minister promises to last (8)
PREVIOUS (P REV IOUS)
hypotenuse score side dozen marvin's marvelous mechanical museum almost year over previous.
"Hypotenuse score side dozen" seems like it might be describing a right-angled triangle with hypotenuse of length 20 and one side of length 12; the other side is then also of integer length, namely 16. Maybe the combination is some permutation of 20-16-12? But we still have the other answers to consider.
After a nudge from OP in comments,
it looks to me as if successive groups of four clues yield the three numbers. If the four mentioned above yield just one number then I suppose it has to be the third side: 16. MMMM must refer not to the (rather obscure) museum of that name in Michigan, but to the album named after it, from the (rather obscure) band Tally Hall. This has a track called "13" so that's probably the next number. Finally we have "almost year over previous"; I guess "almost year" means 364 and "previous" means the number we just found, so 364/13 which equals 28.