I have been running a Megajolt, 1800cc XR3i Zetec on Fireblade carbs with no problems and no filter.
Last week I fitted an ITG Megaflow filter and now it's running like a 3 legged donkey.
When asked for full throtle it does not respond, it misses and does not rev,
but when u ease your foot off it picks up and revs to the limiter.
Does this mean that I should fit smaller main jets as I have disturbed the fuel air balance in favour of the fuel.
It was on 170s but I increased them on the advice of the local Weber agent who loaned me 180 main jets.
This has helped get rid of the midrange misfire but still no top end. It is the filter as I have no problems when I take it off.
What are other people using in the bike carbs?
The map I'm using is for twin Weber 40s and was working ok.

180's will almost certainly be too big. I run 170's in my 2.0L zetec / blackbird carbs with a pipercross airfilter. I think you'll probably need something like 160 or 165 in an 1800 zetec.

If it is fine without the filter it won't be ignition related. If the map is fine without the filter then leave well alone.
The jets sound too big, I had 160s in my Pinto and that was too rich.
Are you sure the filter is clean and not clogged up. Give it a clean in some petrol.