I'm no expert on ZM having yet to finish one. Hell, I'm no "expert" on much of anything.
I do not think paint thickness is your issue, maybe a contributing factor, but not the only issue. On my Bf109 and J2M3 the destructions had the engine built a day or few weeks before these panels get attached. I assume you did the same?
On both of mine, there's no jig or even measurement (down to 100th of a mm?) of where your engine mounts should be in relation to each other. Yet I think it is that important as the glue and paint cure to hardness.
On my Messerschmitt, I did have some issues with the cowl panels closing the gaps. Now mine was an inverted V-12 not a radial, so my bigger issues were where the cowl panels covered the exhaust. I chalked it up to the fact that the cowl panels I chose to use were the "open" version and that meant they would not fit right in the "closed" position. Those closed parts are still on the sprue.
However, with the MGs on top of the engine, they were square with the block and all was good, the engine mounts looked good too. Until I mounted the engine mounts to the firewall, and they were skewed!
I', getting close to attaching the cowling around my other ZM kit with a radial, and that older kit does not have a provision for "open" cowl. I'm a bit worried I'll have the same or similar issue. But I'll keep you updated.
Here's my current state...
View attachment 134158
Well not quite, I did attach the other half of the fuselage.
View attachment 134159
But I think these pictures show what I mean about the faith you must have that the engine is mounted correctly, with no good way to be sure.
That is IF you follow the destructions completely. I'm thinking I'll be using the cowl panels to test engine mounting for any future ZM kits. I do love their approach!