SMPS transformer issues
It seems to me that you are confusing some things. The two primary windings are on the LEFT in the schematic, pins 1-2 and 3-4. The two on the RIGHT, are secondary windings, pins 5-6-7 and 8-(9).

The 2nd primary is for the 5V supply for the digital supply. It's pins 3 &amp; 4 on the schematic

It doens't work that way. In a transformer, all the coils influence each other. If I understand the schematic correctly, the primary coil that 'does all the work' (power goes IN) is the Pin 1-2 winding. The 3-4 primary winding is for feedback and power for the primary switching transistor/circuit. So although it's on the primary side, power doesn't go IN, but OUT. I'd call it a primary winding, because it's on the live side of things. But maybe to call it that is wrong, and it should be called a secondary winding? I'd be interested to learn how that works actually. I guess it depends on how you look at it.

primary one (pins 1 &amp; 2 ) is from the mains
Primary 1 ... pins 3 &amp; 4 was approx 44 winds

Let's stop the confusion, and call Pins 1-2 Primary 1 (P1), and pins 3-4 Primary 2 (P2). Pins 5-6-7 Secondary 1 (S1) and Pins 8-(9) Secondary 2 (S2). Maybe you should edit your post to match...
So count the windings of P1. Then count the windings of S1. This should be something like 9:1:1 (for 50% duty cycle at 165V). So for every 9 winding on P1, S1 Pin5-7 has 1 winding and Pin 6-7 has 1 winding (2 windings in total). Of course there are guestimates, the actual amount depends on the desing of the SMPS. Also take note that the direction of the turns matters!! The turn direction is marked by a dot in the schematic.
Then for S2, you still compare with P1. This should be something like 33:1 (again, for 50% duty cycle).
Update: Apparently this SMPS has quite a low duty cycle at 165VDC, see corrected values at UPDATE below.
I don't know about your broken E-coil, but I'd say to glue it is a long shot, and you'd be better off with a new transformer... But I might be wrong.
Also note that not all broken parts will seem 'burned'. Usually the main switching transistor blows, taking more parts along with it. You can't always find the faulty parts by eyesight.
I hope you'll be able to fix it. Just make sure you insulate the primary windings from the secondary ones properly. Use the right tape for it, as your safety depends on it!
Hope this helps. Good luck!

UPDATE:
So the correct number of winds should be:

P1 (pin1,2) has 44 winds
P2 (pin3,4) has 2 winds
S1 (pin5,6,7) has unknown winds
S2 (pin8,9) has 4 winds

 

Up1:Us2 = 165:5 = 33:1
P1:S2 = 44:4 = 11:1
33/11=factor 3

 

Up1:Us1 = 165:18 = 9:1
divided by factor 3 gives you:
P1:S1 = 3:1

Since P1 has 44 winds, 44/3=14.7 (approx. 15). That would mean that S1 should have 15 winds for 18V (so 2x 15winds for 2x 18V -or- 15 winds between pin6-7 and 15 winds between pin7-5)
You can read more on how it works here

About turn direction:
Look at the dot in the schematic. If you connect the start of the wire to the dot, start turning in one direction, say CLOCKWISE. Then for the other coils, also connect the start of the wire to the dot and start turning in the SAME direction - in this case I chose CLOCKWISE. This way you'll do the direction right. You can also choose to turn CCW, but then you should do the other coils also CCW.
IMPORTANT
The dot on P2 is in the wrong position. The dot in the schematic should be on pin4, and NOT on pin3!
About dot notation:
Yeah, the dots... there's so much confusion about them, and I've looked at many schematics online only to find so many dots in the wrong place.

P1 is the coil that creates the magnetic field. The + is connected to the dot, so current flows from the dot terminal to the non-dot terminal. Remember that.
S1 is a coil that does the opposite. It turn the magnetic field into a current. Here, the current flows in the SAME direction, so from dot to non-dot. To make that happen, the + must be at pin 6.
Same for S2. Current flows from pin9 to pin8, so the + must be at pin 8. That matches with D8 and D10, otherwise nothing would happen.
For the + to be at pin3 of P2, current must flow from pin4 to pin3. So the dot must be at pin4.