yzf r125 new engine. not starting

ok so i just had a new engine replaced 400 miles ago even though it was fine ( the problem was the fuel pump! ) now my bike wont start. its trying really hard to go. popping and spluttering like its justr cold or something. bike has been running perfectly. i cut the baffles of my exhaust and thats when the problems started. it started taking longer anf longer to start ( would start asap when warm ) when cold until eventually it wont go at all! jumping and bumping is a fail. anyone have any ideas? please help. just lost my job and cant afford the garage bill :/