99 R1 project cuts out

Hey everyone,

First off let me start by saying I'm new to the forum. My name is Chris, just picked up this 1999 Yamaha R1 for cheap.

Needed some electrical work and some tlc.

Its running good now, got out on the bike tonight after changing the oil and filter, putting new plugs in and getting the plastics back on.

I noticed once I get past 1/2 throttle the bike likes to cut out. Apparently the bike is jetted for the header and exhaust on it. Carbs are fine (as far as I know).
The bike starts and idles/runs fine up to over 1/2 throttle and then it likes to chug or cut out.

I'm curious as to how much of an effect a hacked up airbox might have on this. The guy before me cut the "tubes" off the top of the air box to "allow" more air in. He then screwed a metal plate on top for some reason over those holes to not let anything fall in is what I'm assuming.

Could that possibly be a problem? Like I stated it runs/rides fine up to about 1/2 throttle then it will chug.

I apologize for the novel, hopefully someone can shed some light as to where to start to look.