so its possible to used the 1098 loom, canbus based clocks and ECU then have the ecu remapped for that engine/exhust fuelling/ignition etc by someone like CJS?

Maybe but the 998 does not have some of the sensors that the 1098 has so the canbus would possibly not work? Also I bet many of the plug connectors are different so a lot of splicing would need to be done.

If you have no 998 harness the next best thing is a 620/800 harness almost a straight fit apart from the coil plugs.

I have a mint 620 harness for sale.

http://www.ebay.co.uk/itm/2814265290...84.m1555.l2649

Pretty much, a few wires need swapping, the 998 doesn't use the idle control, exhaust valve or Lambda probes.
Speedo needs a sensor off the rear wheel if it's going on a road bike.

Decoded clocks or a set with matching keys may be needed if using a standard ECU. As in my experience the Can Bus seems unstable otherwise as the data stream isn't complete.

thanks gents very informative
so does the 620/800 loom uses the 3 pin coil connectors vs the 998 2pin?

You could use the 620/800 coils if you have them. I have the 998 ones and they are both 2 wire but spade connectors on the 620 and a 2 pin plug on the 998 so just a case of adding the plug if need be. Apart from that everything else seems to correspond ok.
Theres gonna be bit of tweeking as regards routing and mounting but no big deal.

My 998 harness (if you can find one) cost me way over twice what I want for the 620 one. :o