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I've managed to blow 3 ignition coils on my '89 twin plugged R100, These are the PVL twin output ones.
Why are they blowing? should I not use suppressed plug caps?

I doubt suppressed caps are the cause.

What is the coil primary resistance ? Very low resistance coils will only survive if driven by an ignition unit with appropriate dwell control to stop them over heating.

Since the bike is twin plugged are the wires matched as far as resistance? Are you running stock points ignition or an electronic replacement?

This is an '89, guys----no OE points ever involved. Resistor caps are recommended; resistor plugs are not. As usual, Snowbum has a treatise http://bmwmotorcycletech.info/Ignition.htm

What exactly was the failure mode of the coils. Did the primary winding fail or the secondary winding ?

Failure mode - a brown sticky stuff blew back over the engine cases - how to test them for each winding? - tell me how.
How do you balance the resistance of the plug leads other than make both cylinders have the same sum lengths?

To test which winding has failed you need an ohm meter. Any cheap digital meter will have an ohm range. The primary winding which is where the two wires from the wiring harness connect should measure approx. 1.5 ohms. The secondary winding which is across the two HT terminals should be something like 10,000 ohms. Brown sticky stuff sounds to me like the coil overheated and the insulation broke down. Any idea what model PVL coil they were so that the specification can be compared to a stock coil.

I wouldn't fuss about the HT leads or caps. As long as they are not excessively high resistance or completely open circuit, minor differences in resistance can't damage the coils. If it is the HT side that has caused the failures it will show up on the resistance test of the secondary windings. My money is still on the primary windings but the tests will show which it is.

These are probably similar to the PVL coils Moto-bins sell?

(I couldn't get a direct URL to work showing this part, but it is their part no 70506 listed among their ignition coils for 2-valve twins)

I found a used pair of those when twin plugging my /7; unfortunately one of them only fired one plug so I left them in my parts bin. Checked them now, they have a primary resistance of 1 Ohm, and secondary 8 kOhms. Mine are also filled with a red-brownish insulation mass, which I guess melted in Nourish' ignition system.

Would be interesting to hear which ignition system was used.

I remember having read a warning somewhere about not leaving the ignition on without starting the engine, since current would/could flow through the coils and result in overheating - but not sure now which system this was.

The reason I've been guessing it's a primary winding failure is because I suspected they might be the Motobins coils. According to Pazon ignitions they are in fact 0.6 ohms primary resistance which is much too low when used as a single coil but might just be OK if two coils were connected in series for dual plugging bearing in mind the ignition system was designed for 1.5 ohms.

Coils of such low resistance need dwell control to survive and would overheat quickly if the ignition was left on and there was no automatic shut off. Whether or not the BMW ignition module has these features is very fuzzy. The very latest purple one is supposed to be OK.