@DeeTeeArr Definitely do a full carb clean including the emulsion tube (the brass tube the main jet screws into). A lot of people (including bike shops) miss this and don't realise it comes out because you have to screw the main jet back in without the brass washer and tap it gently to remove it from the carb body. The space between this and the carb body gets blocked with moisture, dirt etc and blocks more and more holes in the tube (which is how the air atomises the fuel) until it just starts fourstroking and won't rev out one day as this controls the mid-throttle fuelling. Just chucking it in an ultrasonic cleaner usually isn’t enough; you have to actually remove everything from the carb body, physically make sure all the jets and air passages are clear, then reassemble. Make sure the air supply to the emulsion tube is clear as well, it's the small brass tube on the right of the carb body just in front of the carb-to-airbox rubber. You should be able to blow through it, but only just.
I'd also echo what @calum said; it shouldn't really be necessary to re-jet just for a DEP exhaust and the OEM TM28SS is the best option for the DTR if you can save it. It's well worth soaking the carb body and all the jets in alloy wheel cleaner for a day or so as this always brings carbs up like new even when people restore bikes twice the age of the DTR.