The jetting wouldn't cause it to overflow/flood like that.
I woulds start the jetting with the main jet at stock +2 sizes richer for the FMF exhaust. Are you getting the roundslide carb from ebay?
If so, stock jetting specs are as follows: #142 main jet, #52 pilot jet, jet needle 2nd groove from top, airscrew 2 turns out.
Again, these are stock baseline jetting specs for the '85 model with the roundslide carb as stated in the Honda
service manual. I would go with a 145 or 148 main jet to start with and go with the stock size pilot jet (#52). Just running an upgraded exhaust rarely requires a pilot jet change.
You may also find that you will need to raise the jet needle a tick or 2 as well. Might even be a good idea to raise it one notch to start with anyway. Better to start rich and work your way leaner to dial it in. Sparkplugs are cheap, topends are not.
And as to where to get your jets. Any dealer/motorcycle
parts shop worth it's salt will have them on hand or at the very least be able to get them for you easily. There are places online too. Might be a good idea to order a complete jet kit and have an assortment to work with. Just be sure and order jets for the right carb. Between the '85 roundslide carb and '86 flatslide carb the main jets are the same, but the pilot jets do not interchange. If you have the roundslide it is a type "PE". So you would then want a jet kit that has jets that work with the Keihin "PE" carb. The '86 flatslide is a type "PJ". And of course if that is what you have you will want jets that work in a "PJ" carb.
Oh, and a .040" overbore should require minimal (if any at all) jetting changes.... So a little on the rich side of stock jetting should work fine. But as I said, start rich (148 main, raise the needle 1 position) and work your way leaner.