4048 Rules of Construction by Poat

This was a superbly constructed puzzle by Poat. The problem of unchecked letters in jumbled entries was resolved as soon as the solver realised that there was a word square in the grid. The central 8 by 8 square contained the same words across as down.
BACKACHE
APHELIAN
CHARACID
KEROSENE
ALASTRIM
CICERONI
HAININGS
ENDEMISM

The extra words in clues were – young people, fish-eating bird, movement upward, school absentee and organ rupture. These defined five elements of a six-letter word square. The missing element has to be SYNTAN or SYNTAX. The Title is the decider, as Chambers defines syntax as ‘a set of rules for combining the elements of a programming language into permitted constructions’

YOUTHS
OSPREY
UPTURN
TRUANT
HERNIA
SYNTAX

Across
1 Robin's band loses a member, good lord! That's a pretty picture (12, two words)
MERRY ENGLAND MERRYMEN less M (member) + G (good) + LAND (US slang)
9 Skinhead busted? Somehow we've succeeded in this trap for [young] rogues (5)
KHEDA Compound Anagram SKINHEADS less S (succeeded) + IN
11 The tipple of party [people] with a sophisticated air (7)
CAMPARI CAMP + Anagram AIR
12 [Fish-eating] sailor educated amid the oysters? (4)
ABED AB (able seaman) + ED (ref. Oyster beds)
14 One might get thick ear from this courthouse, given time (7)
KACHERI Anagram THICK EAR less T (time)
15 "Fawn" lady traps a number of deer (8)
ELAPHINE ELAINE (meaning FAWN) containing PHI (Greek numeral)
18 Leaders in Eurovision Song Contest hold a rally in Slough (6)
ESCHAR Initial letters; ESCHAR is a slough
20 Top teacher in charge of mythological [bird] books (5)
EDDIC EDD (Doctor of Education) + IC (in charge)
21 Jack of old turned to serve master, former King (5)
MAKER KA (serve) + M (master) reversed + ER (King Edward)
22 Newton enters to learn about philosopher (6)
SENECA N (Newton) in SEE + CA (about)
23 Take a bow together, engaging wing [movement] (6)
SALAAM ALA (wing) in SAM (together)
25 21's place for hawking, getting money for very little (5)
RIMER RIVER (place for hawking) changing V (very) to M (money) (21 MAKER = poet)
28 Central clump of narcissus starts to crowd out Lakes resident (5)
CISCO CIS (central letters of narCISsus) + C(rowd) O(ut)
30 I'm backward and not [upward], in fact (6)
MAINOR I AM (reversed) + NOR
32 Securing one ruling member in Chinese government (8)
CHAINING A IN (ruling member) in CHIN. (Chinese) + G (goverment)
34 French newspaper with a twist? So it would seem (7)
LEMONED Anagram LE MONDE
36 Struggle for fat fighters, the whole coming to nothing ... (4)
SUMO SUM (the whole) + O
37 ... as a piece of cake, dainty French one is devoured (7)
CUNEATE UNE (one in French) in CATE (dainty)
38 Means of punishment fit for prisons, when depleted of oxygen (5)
JOUGS O (oxygen) in JUGS
39 Sweet temper suffusing Zeus, transfigured in Minotaur's home (12, two words)
CRÊPE SUZETTE CRETE (home of Minotaur) containing Anagram ZEUS in PET (temper)
 
Down
1 Finish [school] break without marks for easy living (9)
COMMENDAM END (finish) in COMMA + M (marks)
2 Partly recover from spider in Oz (not dead) (6)
REBACK REDBACK (Australian spider) less D
3 Woman's cycling round accident in junction (6)
RHAPHE HER (cycling to RHE) containing HAP
4 Dieter's egg needs potassium as supplement (3)
EIK EI (German for egg, Dieter is a man’s name!) + K (potassium)
5 Teach as [absentee] left and ran amok (4)
LARN L + Anagram RAN
6 Organic ice could be bad for one's teeth (10)
CARIOGENIC Anagram ORGANIC ICE
7 Improve energy -- that would be fine (6)
AMENDE AMEND + E (energy)
8 Repulse, beating out desperate character in fortification (5)
REDAN REPULSE less PULSE (beating) + DAN (ref. Desperate Dan)
10 Dropped pipe [organ] down a couple of notes (4)
SHED SH (pipe down!) + E + D (2 notes)
13 Fish biting in a river, each in a frenzy (10)
CHARACIDAE ACID (biting) in Anagram A R (river) EACH
16 Rail provided enclosure (5)
SOREE SO + REE
17 Set up surfing aid, one using echo-location? (9)
REARMOUSE REAR (set up) + MOUSE (useful when surfing the web!)
19 Quiet recurrent melody, a line held by the flutes (5)
STRIA ST (be quiet) + AIR reversed
24 Bird tucked into ripe fruit (6)
ACHENE HEN in ACE (excellent = RIPE)
26 Is Gone With The Wind simply stylish? (6)
 SOIGNÉ Anagram IS GONE
27 Keeping quiet about it is ______ (6)
MUTISM TIS in MUM; & lit.
29 Punish Wimbledon's ten fools about this? (5)
SCOUR TENNIS COURTS less TEN NITS
31 Energy in a dog's tail, eagerly excited (4)
AGOG GO in A (do)G
33 [Rupture] giving a dart of pain, nurse takes temperature (4)
STEN  T in SEN
35 Workers requiring uranium for nuclear plant (3)
MEU MEN less N (nuclear) + U (uranium)