So the question is this. In normal use and with hot engine 
compartment temps together with baking in the sun, do bubbles 
eventually start to form and become visible in the paint, especially 
on the upper cowl???

Angier,

 

No.

 

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Should I remove the gel and fill all voids.
>>>

 

Ideally, yes.  Practically, no.  Just fix the voids as you find them. 

 

The LNC 2 cowl and wingtips are made like a cheap boat, loose weave glass mat and gel coat (ugh). You should consider:

 

1. Adding a layer of finer weave glass or carbon around the edges where fasteners are to be used.

 

2. Sealing the inside of the cowl to stop oil from penetrating and perhaps lifting the paint.  If the paint is white is make finding leaks and rubs much easier.

 

3. Applying heat reflective material in high heat areas, such as where exhaust pipes run close to the cowl.

 

Treat your cowl with love and respect and it will serve you well grasshopper.