Fitting the airbox lid restricts the airflow, so the bike will run richer. If it runs properly without, and badly with, then I'd suggest that it has large jets in there to match the extra air flow.
Have you removed the carbs and checked the jet sizes?
If you simply fit tyga pipes to a stock bike with stock air filter, you will probably get away with stock jetting, especially on an unrestricted MC18. Obviously you need to know what's fitted now, and adjust them accordingly once you have the intake setup to your requirements.
The TYGA pipes generally make peak power just below 12000 in my experience - a good thing for engine life!
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