3923 Family Planning by Brimstone

This was a nice challenge. The double extra letters in across clues meant that you had to solve a lot of clues before the message became apparent. Taking these letters, one at a time, twice from across and then from down clues gave this: "The Third Man, Orson Welles. In grid change output from Italy to that from Switzerland" This referred to the famous quotation; "In Italy for thirty years under the Borgias they had warfare, terror, murder, bloodshed - they produced Michelangelo, Leonardo da Vinci and the Renaissance. In Switzerland they had brotherly love, five hundred years of democracy and peace and what did that produce? The cuckoo clock!" So it was a pleasing discovery to find that by replacing RENAISSANCE at 34 to CUCKOO-CLOCK, you still had real words in the downs. The unused letters in the seven-letter clues could make THE BORGIAS, thus explaining the relevance of the title.

Unused letters are shown in square brackets.

Measure air-pump skill ARE AERAT[O]R ART
Cut sow refiner AXE ELT EXALTE[R]
Fish branch debt [G]OURAMI ARM IOU
Age provokes family ELD KINDLE[S] KIN
My clear brownish-yellow COO RID OC[H]ROID
Encloses before cat INS PRE PERSI[A]N
Whisky money truth RYE LAT REAL[I]TY
Mistress notices chest MRS R[E]MARKS ARK
Maid eyes ribbons AIA EEN [T]AENIAE
Plant hail rush VER[B]ENA AVE REN

1A book coming as relief after collieries (6)
PSALMS p[it]s + alms
4 Dotes on horse and is troubled (6)
ADORES anag. [h]orse a[n]d
8 Tackle, one leading to a strain (4)
ARIA [ge]ar + I +a
9 The old recommend blowing vest with air (5)
AVISE anag. ves[t] ai[r]
11 Hide locally, being on income support for season (4)
SELE [h]ele (now dialect) to hide, with [I]S income support
12 Doomed father dug tunnels (6)
DAMNED da[d] m[i]ned
14 Discharged old one from monastery (5)
LOSTE [c]loiste[r] minus I (one)
15 Ground hog day exercises (4)
anag. [h]og [d]ay
19 Vehicle is pursued by murderer with compound eyes (not English!) and growths (11)
CARCINOMATA car C[a]in (the Biblical murderer) om[m]ata (compound eyes)
21 As you would expect, four canoes capsize (8, two words)
OF COURSE anag. four c[an]oes
22 Defeat secret society on the outskirts of Kowloon (4)
TONK To[ng] (a Chinese guild or secret society) K(owloo)n
30 Smooth love scheme (4)
PLAN plan[e] =smooth [O] love
31 Scorpion perhaps found in fruit of oak with hard inside in dry surroundings (8)
ARACHNID the large class of arthropods that includes spiders, scorpions, mites, etc.
arid (dry) round ac[or]n with H (hard inside
34 With a bit of sympathy nuisances are reformed in a new beginning (11)
RENAISSANCE anag. S(ympathy) + n[u]isance[s]
37 Trap with shepherd's pipe. Ingenious! (4)
NEAT (ingenious) ne[t] [o]at
38 Shaggy page provided workers (5)
MANED [P] page + ma[n]ned
39 A worker, name unknown, follows current prime minister (6)
INDIAN a person who carries out orders, a worker, etc,
I (current) N[U] (name unknown) di[w]an (Indian minister)
40 Thanks is given always for possessions handed down to us (4)
AVER (possessions) [t]a =thanks [e]ver=always
41 Ineffective war of intercourse? Look to end sexual affair (5)
LINGO Rather obscure definition. Chambers gives - a language, esp one poorly regarded or not understood; [f]ling + [l]o
42 After practical jokes set fire to door (4)
EXIT [r]ex (an obscure word that often appears in Listener crosswords) [l]it
43 Those yet moving around moon (6)
TETHYS a moon of Saturn. Anag. th[o]se y[e]t
44 Judge donkeys and manuscripts (6)
ASSESS asses [ms]s manuscripts abbr.

1 Manuscripts brought forth from hill year before in Italy (6)
PAPYRI pap (hill) yr (year) I (in) [I] Italy
2 Priest, Roman Catholic Knight Templar and evolutionist (7)
LAMARCK lama (priest) RC (Roman Catholic) K[T]
3 Busy chap has international account (5)
MANIC man + I + [a]c. (account)
5 Efface part of model letter (4)
DELE hidden del[l]e
6 Grass hardens and receives stolen goods (6)
RESETS (receive (stolen goods) knowingly) r[y]e + sets
7 Broadcasters making ends meet on Sabbath (8)
SEEDSMEN anag. ends mee[t] + S9abbath)
10 Confirm truth about Foreign Office excluding Thailand (6)
VERIFY veri(t)y round F[O]
11 Child takes sailors' underwater detectors (6)
SONARS son + [t]ars
13 Brush hard on black space (5)
BROOM [H] + B + room
16 Thin relation is after silver (5)
GAUNT [A]g (silver) + aunt
17 At a former time, people of fashion seen at front of church (4)
ONCE [t]on (fashion; people of fashion) + CE (Church of England)
18 Send out flare. Make a defensive ring (4)
LAER anag. [f]lare
20 Dark unfinished precious material for vases presented to King (4)
MURK mu[r]r(a) + K (king)
22 Old bird put in cake. It's put under the plate (8, two words)
TABLEMAT m[o]a (extinct bird) in tablet
23 Gunners take most of old fortified site but it's of no value (4)
RACA RA (Royal Artillery) + ca[m] (see kame)
24 Cut back on energy for room (5)
PLACE [s]calp rev. + e (energy)
25 River pottery is excellent (4)
RARE R=river + [w]are
26 Limper, leaner, mostly cross inside (6)
LANKER l[i]er with ank(h) inside
27 Dilute G and T creating a problem (5)
THING thin=to dilute + G & [T]
28 Handle found in South Africa and North and South America (4)
ANSA [Z]A (S. Africa) + N + SA
29 Getting up without getting into clothes (6)
RISING sin[e]=without inside rig
30 Worried spinner conceals drug money (7)
PENNIES anag spinne[r] + e=ecstasy Drug usually indicates E or H (heroin)
32 Old apple left to take orange-brown colour up (6)
RENNET [L] + R (take) + tenné (rev.)
33 Anthems sung with return of intoxicating juice about lunar new year festival (6)
MOTETS tet in SOM[A] rev.
35 Shame boy has to revert after help (5)
AIDOS so[n] reversed after AID
36 With little effort take head off alcoholic drink (4)
IDLY (t)id[d]ly =an alcoholic drink