OK - all sorted. Seems the EML light was unrelated to the exhaust install - just coincidence. Cylinders 1-3 misfiring - coils diagnosed and replaced (4-6 also) with new spark plugs.
Incidentally, I have a Warranty Direct policy on the car and, good news, coils are covered. However, due to £50 excess, 30% parts contribution (age of car), and the fact that they won't cover cylinders 4-6 as not failed yet they will cover less than half of the £500 cost! I was thinking of cancelling before, but definitely now. I think only worth if you are expecting a big fail with a £1k+ bill...