First - on plastic, I use a plastic putty. Squadron makes an excellent one. Testors, Tamiya, Gunze (and I would assume European brands like Humbrol and Revell Germany) make some as well. It dries fast, is easy to form and remove excess and forms a physical bond with the plastic (just like solvent cements do).
Another option are the 3M putties. Those I use for smoothing transitions that you mention. They are an acrylic putty that was engineered for use in the automotive industry to smooth small dings in body work as well as a modern replacement to old school window glazing putties. They are readily available and pretty easy to work with. Red is what I have on my bench right now, but I have used blue and white as well and they work in the same way.
I only use epoxy putties with resin or metal for joints.
Second - Micromark or Widget's Supply have some of the largest selections of small files and the prices at Widget's are excellent:
http://www.widgetsupply.com/category/file-diamond.html
http://www.micromark.com/filing.html
The needle files should work the part for you. You may be able to find them at local hobby or hardware stores too - though that can be hit and miss and come with the B&M premium prices.
Thirdly - time to look at a seperate applicator. Almost all the adhesives which I use are capillary cements/solvents. That is you apply a very little to the joint and let physics carry the liquid where it needs to go. The nozzles on those bottles provide a similar method - but because you are holding the bottle with the nozzle...it is very easy to get too much. Instead look at a regular bottle of cement (normally glass bottles with a screw cap - Tenex 7R is an excellent one for styrene plastics) and couple that with a seperate applicator like the Touch-N-Flow:
http://www.micromark.com/touch-n-flow-applicator,7841.html
The needle is much finer than the needle on the bottle combos like you are currently using and the flow is entirely by capillary action so it will only draw out enough to do the job.
For working with
CA glues on metal and resin - I use a similar tool which allows me to have much better control over the glue and prevent more getting out than I need.
http://www.micromark.com/micro-glue-applicator,8048.html
As always - your own preferences and habits will dictate things some. As will geographic locations regarding sources.