Ideally, the cowls should not require much finishing work. They are popped out of a mold. Anything popped out of a mold should not require much filling and sanding. If you've matched the cowl surfaces to the firewall, strakes, and wing roots, you can most likely skip the micro filler and go straight to applying the high build primer.
However, my cowls will require more finishing work than usual. First, I modified my cowls substantially. Second, I found that my cowls did not match perfectly to the plane after the wings, strakes, and turtleback were contoured. There were slight mismatches at the wing roots and at the aft edge of the strakes due to the slight thickness of the micro. Last, the general workmanship on these AeroCad cowls is terrible. There are many air bubbles in the plies and various other voids, bumps, and bruises. Plus, the exhaust holes do not line up. These all must be fixed, filled, and sanded.
I did not want to add a lot of micro filler to the cowls. The cowls are really flexible. They're put on and taken off all the time. They are handled alot. Micro filler will crack and chip if it's too thick. Micro fill should be kept to the bare minimum. So, I took the time to realign the cowls to the plane. I added of few plies of BID to the wing roots to raise the cowl slightly and match it precisely to the contoured wing roots. I cut off the parts of the cowl flanges that go under the spar flanges. I made new ones that realigned those edges to the contoured strakes.
Here are pictures of the contouring on the bottom cowl. (The top cowl is similar.) Bottom cowl fitting and contouring is best done with the plane upside down. The second picture shows the process for precise alignment. I applied strips of duct tape to the wing roots until the cowl matched the wing root. Since duct tape is almost the same thickness as BID, the strips gave me a good idea of where to apply the BID plies.
Once the cowl was refitted, I filled a one-inch swath along the wing roots and filled 3 inches on each side of the cowl-strake and cowl-turtleback junctures. Once the micro cured, I contoured all the micro and opened up the gaps with that same perma-grit file I've used on all the other gaps.
This is the next problem-child that must be fixed. Again, the workmanship of the AeroCad cowls is horrible. The exhaust ports on the lower cowl do not match up AT ALL with the ones on the top cowl. The plan is to cut out these ports, install the engine, shape some blue wing foam around the exhaust pipes, then use the foam as molds to rebuild the cowl exhaust ports. I may also add a boat tail onto the lower cowl, depending on how it fits with the engine. We'll see. Stay tuned.