most likely, you tweaked one of the TX mixer cans to the point where it wouldn't pass enough RF for the next stage, thus killing the output.
first thing is to do the PLL alignment with your scope, peaking those cans like the manual says.
then use your scope on the output of each TX coil. start with L23, and peak the coil in TX mode for max indication on your scope.
then move on to L21, then L20, then L17, and then L14.
the reason to do it that way is because you may have one coil so out of whack that no matter the tweaking you do on another coil upstream, you can't see an indication on the meter.
refer to this schematic:
http://www.cbtricks.com/radios/cobra/29ltd_29ltd_st_29wx_st/graphics/cobra_29_ltd_classic_sch.pdf
i will give you the points to hook the scope probe to since you are new to this, but setting the scope properly to see the output is up to you. there are many places online to show you this.
for L23, connect the probe to pin 4 of IC3.
for L21, connect the probe to pin 7 of IC3.
for L20, connect the probe to the junction of R61, C85, and TR16.
for L17, connect the probe to the junction of R58, C155, and L17.
for L14, connect the probe to the junction of L14, L13, and C59.
i have a feeling that it's either L20 or L17 that is the culprit, but its just that, a hunch.
if you get to a coil that doesnt seem to respond at all when you turn it, stop there and post back here.
yes, there is a chance that you smoked the driver or final, but we can check that next.
there are much more knowledgeable people here on this forum than me, so if you get other advice that tells you to go in a different direction, their advice should be heeded also.
LC