that would not affect the mot, provided you have legal exhausts with baffles on, if the rest of the bike is tip top you will be fine, I've done 2 mot's with stage 1 & 2, PCIII and stubby cans, never had a problem, however do check the following things that mot testers are looking for recently:

all lights, indicators, stop light to work, brake pads wear, tyre wear, chain/sprocket wear.

Good luck