From what I can tell, your bike came with 148 main and 55 pilot jets, and a 2.5 throttle valve. A 140 main seems pretty lean to me. I'd put the needle clip is in the center (#3) position to start, if it's not there already.
Have you set the float level? This can make quite a difference at low to mid throttle settings. My Clymer manual indicates the correct height is 20mm. and the adjustment procedure is in the link below, page 42 (actual page 46):
http://honda-elsinore.alp-sys.com/manuals/MR25076/ShopManual76mr250.pdfDoes adjusting your air screw have any effect? It should help with your idle and low-throttle operation, possibly a lot (2.5 turns out max). A 52 pilot might help even more.
I've only jetted this carb for a 125, so someone with 250 experience should have better info.
Ray