3990: I Know My Place by Syd Lexis
 
This was an amusing puzzle from Syd Lexis. It soon became clear that the letters omitted from wordplay lay in the diagonals. In the preamble we read, “Resolving Syd's crosswords will show that he knows his place, accepting that others are more knowledgeable than he.”
The diagonals gave most of the acronym Y(Y)URYY(U)BI(C)URYY(4)ME which can be read as -
Too Wise You Are, Too Wise You Be, I See You Are Too Wise for Me
This allowed the 4 unchecked cells to be filled. For Gregson this was made easier as the phrase had recently appeared in an article on text-messaging. It will be interesting to see how other solvers found it.

Letters omitted from word play are shown in square brackets.

ACROSS
1 Oriental aged, turned back (7)
EASTERN AE (reversed) + STERN
6 Let him take a fine tobacco (4)
CAPA CAP (let him take) + A
11 With missile part I bombed soldiers (12)
IMPERIALISTS Anagram missile part I
15 Milton's destination -- ravine in Lydford, maybe (5)
GOYLE (SW Eng. dialect; Lydford is in Devon) GO[Y]LE = GOAL (Milton)
16 Shakespearean shoots up, cheers (7)
SPIR[I]TS SPIRTS
17 Defeat payment security system ... (3)
SET  2 definitions: Secure Electronic Transaction, a credit-card payment security system on the Internet.
18 ... a tangle from beginning to end (3)
ORE 2 definitions ORE  and O'ER
19 Propagate cocaine in medicine (7)
TRAD[U]CE C in TRADE
23 Ossa broken? Lean ... (5)
[U]LNAE anagram LEAN
25 ... on Henry: drink is healthy (4)
HALE H (Henry) + ALE
27 In Scotland rattle a devious person (4)
[R]EEL EEL
29 Motor race in Germany (4)
IND[Y] IN D (Germany)
30 An ecumenical group does something ... (4)
ACTS Action of Churches Together in Scotland.
32 ... biblically ingenious with one abstainer (5)
WITT[Y] W (with) + I + TT
34 Cow's mood finally stressed (7)
OX[Y]TONE OX + TONE
35 Queen's one starting to enjoy form of public service (3)
USE US + E(njoy)
36 One's avoiding old pike when in Perth (3)
GED AGED less A (one)
40 Postponed case about American capture (7)
RE[M]ANET RE + A (American) + NET
42 Titmouse regularly failing to colour deeply (5)
IM[B]UE even letters tItMoUsE
44 Chaotic doings stain names (12)
D[E]SIGNATIONS anagram DOINGS STAINS
45 Fighter was at the front of repulsed charge (4)
DELF F + LED (all reversed)
46 In Russia spiritual adviser begins an argument after swallowing ecstasy (7)
STARETS E in STARTS
DOWN
1 He hit Gs, playing octaves ... (7)
EIGHTHS anagram HE HIT GS
2 ... in a frenzy, a musical variety performer failing to finish (4)
AMOK A MOK(E)
3 Hill permitted climbing (3)
TEL LET reversed
4 Ploughs once before start of summer (4)
ERES ERE + S(ummer)
5 Minced dish, with meat lacking colloidal suspension, is swell for doctor (4)
RISE RISSOLE less SOL
7 Advanced Irish remedy (3)
AIR The clue was impossible to parse until later corrected to
Advanced Irish melody (3) A + IR
8 Pressure is applied to particle (5)
PS[I]ON P + ’S + ON
9 Draw a prize; vehicle is returned before time ... (7)
ATTRACT A TT (prize/trophy) + CAR (rev.) + T
10 ... being two seconds within Jock's sight (4)
ESSE SS (2 seconds) in EE
12 Ozzie provisional driver lass's rear plate -- (5)
P[Y]GAL P (see P-PLATE) + GAL
13 -- fitting with former antipodean bird (7)
APTE[RY]X APT + EX
14 Drink willingly when it's without charge (7)
LIQ[U]EF[Y] Q in LIEF
20 Negative effect from French books (4)
DENT DE (FROM in French) + NT (books=New Testament)
21 New sound is immortal (7)
[U]ND[Y]ING N (new) + DING
22 Powerful temperature's dropped, freezing mixture (7)
C[RY]OGEN COGENT less T (temperature)
24 Earth in Little John's trench (4)
LEAT E (earth) in LAT (abbr. LATRINE)
26 Cordial American bird is educated (7)
ANISE[E]D ANI’S +ED
28 Weak? Exercise more -- according to Will (7)
USELESS USE + LESS (more, (Shakespeare) with an expressed or implied negative).
31 Musicians relaxed, missing party (5)
COM[B]O COMODO less DO
33 Strainer formed from steel mostly (5)}
TE[M]SE anagram STEE(l)
35 Language Dutch introduced to Uruguay (4)
URDU D in URU
37 Rank old menial's tense (4)
ETAT ETA + T
38 Named Australian tree (4)
DITA DIT + A
39 Anthony's right about one ... (4)
RUNT UN (one) in RT
41 ... to trouble the ego in Albania (3)
AIL AL containing I
43 Muslim ruler's agricultural community (3)
MIR 2 definitions