TB sync and trim pots probs

Hi quick question too the knowledgelble folk on the forum , started to check my TB's and trim pots setting with my gas analyser on my Aprilia rsv 2002 57mm edwards throttle bodies , via the two testing points on the headers ( blanking screws removed ) and noticed the rear cylinder was rich but the blanking screw was chocolate brown on the internal side . Yet the front cylinnder was reading weak , but the blanking screw was sooty black coloured.
But then I noticed on the front cylinder the centre plug lead cap loose and broken ( no interference fit ) while I'm waiting for a replacement cap , would this really effect the mixture outputs ?
The TB settings were rear cylinder bypass screw fully in , trim pot at 3pm , and front cylinder bypass screw 1 1/2 turns out from fully seated , and trim pot at 12pm

Run and EVO air box , Edwards chip , Arrow can

Thanks in advance
Eddie

well i had about 2 on the front cylinder and nearly 5 on the rear which is confusing , just wondering whether the broken spark plug lead cap would make that difference cant really test until I have a replacement

Eddie