if you saw smoke, and there isn't a part on the radio that you had to replace because it was burnt, then the modulation transformer is a likely culprit.
transformers have a specific smell when they burn, but you may not recognize this yet.
chances are that you shorted this transformer to ground, and in turn singed some of the enamel coating of the wire.
if this is the case, you will not notice that the resistance of the transformer has changed, but it will be more susceptible to failure now due to the thinner/ burnt enamel coating.
the lesson here is NEVER run your radio without the proper fuse in line.
use a 4 amp fuse, and you will be good for any mod you are doing, while remaining safe.
if you have a really high powered radio (50 watts or so), and the fuse blows on modulation peaks, you can use a 5 or 6 amp fuse in that specific instance, but for general use, a 4 amp fuse is what you need.
you transformer will probably continue to work, but if it gets too hot, it may short and fail on you. however, if you have a 4 amp fuse in line, it will blow before you see the smoke.
here is a good variable power mod for that radio and the 25LTD:
http://www.cbtricks.com/radios/cobra/mods_&_info/graphics/Cobra_Uniden_Var_Pwr.pdf
you can use this one to check over the one you used if it's different.
LC