Fixing the heater box, question on mounting motor

Heater core leaked so I had to pull the heater box. I had to do some significant fiberglass repairs as you can see in the pic to where the motor plate mounts to the box. I have the holes drilled in the fiberglass repair and am going to use little screws/nuts to hold the motor to the box.

I've flat-sanded and filed as best I could without going too much, but the surface isn't perfectly flat for the plate to mount. Does anyone have any caulk or something they could recommend for attaching the motor plate to the box? I don't want it to smell. Also I only need to use a VERY small amount. I have some black RTV silicone (oil resistant type) but doesn't that smell? Or does the smell eventually go away?

I don't want to use sticky-backed foam because again there's only small gaps and I don't want anything pushing against the fiberglass between the motor plate, I just want a thin film of something to fill the voids.

Just use some butyl rubber stips. Napa sells it in rolls.

Flex-seal, RTV, whatever really. They all have some odor until the cure completely. If you covered the motor flange with some material that your gasket maker doesn't bond to ( Shipping tape? ) you could generate a good seal that easily separates again.
The factory used a dense foam as gasket material in a lot of similar places ( accelerator to firewall is one example ). I'm not sure what they used here. You might find a piece large enough in packaging materials,,, Whittle out a gasket.

Wax paper and RTV work real well for making a non permanently sealed surface to surface contact.
I use fast set JB weld a lot for things like that as well.