That's a dynojet kit you have there by the sounds of it. If your spitting flames then it's a sign of running rich, I expect the running rough is bogging down from being too rich also. The flames will be the unburnt fuel spitting out. Also what air filter are you running? If you temporarily take the filter out and it runs a bit better this will confirm it running too rich.
The 3 holes in the slide is that including the one in the centre where the needle goes through or is that 3 lift holes. If that is 3 lift hole then I would block 1 hole in each slide with some epoxy resin. But do a neat job of it or that will upset things.
The best way is to take the needle holder out and put something behind the hole so epoxy does not fall through and make a mess behind and the glue also has something to rest against and dry flush on the rear. A second fill once dry and sand down the smooth on the front. These bikes don't run well with the extra lift hole that Dynojet install instructions say to do.
Have a read through the following on jetting and tuning carbs
http://www.vtr1000.org/phpBB3/viewtopic ... 31&t=14214
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