With a current 10km personal best of 47:40 (4:46/km pace, representing a VDOT score of ~43), your current physiological training zones are:
Easy / Long Run Pace (Zone 2): 5:45 – 6:15 /km
Lactate Threshold / Tempo Pace (Thursdays): 4:38 – 4:45 /km
$\text{VO}_2\text{max}$ Interval Pace (Tuesdays - 5x1000m): 4:18 – 4:25 /km
Speed Repetitions (Neuromuscular Striders): 3:55 – 4:05 /km
Dropping from 47:40 (4:46/km) to sub-40:00 (3:59/km) requires a systematic 47-second-per-kilometer reduction. Shifting your body fat from 14.4% to ~11% (losing ~4–5kg of pure fat mass) will automatically improve your relative $\text{VO}_2\text{max}$ ($\text{mL/kg/min}$), yielding an estimated 15–20 seconds/km speed increase purely through enhanced power-to-weight ratio. The remaining gap is developed through this 12-week progression:
Phase 1: Baseline Adaptation & Fat Loss (Weeks 1–4)
Tuesday (5x1000m): 4:20 /km pace (2:00 rest).
Thursday (25min Tempo): 4:40 /km continuous pace.
Saturday (12km Long Run): 5:45 – 6:00 /km pace.
Phase 2: Threshold Expansion (Weeks 5–8)
Tuesday (5x1000m): 4:08 – 4:12 /km pace (2:00 rest).
Thursday (25min Tempo): 4:25 – 4:30 /km continuous pace.
Saturday (12km Long Run): 5:35 – 5:50 /km pace.
Phase 3: Race-Specific Speed (Weeks 9–12)
Tuesday (6x1000m): 3:52 – 3:55 /km pace (2:00 rest).
Thursday (Tempo): 3 x 3km @ 4:05 /km pace (1:30 recovery jog).
Saturday (12km Long Run): 5:25 – 5:40 /km pace (with final 2km @ 3:59/km).