I would definitely take the time to epoxy prime everything as you are going. From the firewall, under the cowl and the inside (top and bottom) since you are in there. I actually put a single stage urethane on the inside of my '70's cowl over the epoxy when I replaced it. There are several alignment holes in the cowl to assist you in getting it lined back up. I strongly suggest using an export brace to check the firewall positioning before welding the lower in place. Fit everything before committing to welding. If something needs to be adjusted, do it during the fit-up process. I remove the paint from each rosette weld hole with a small wire bush once everything is primed and sheet metal screwed in place. I've installed a couple of these, it really isn't that bad. Pay attention to the details and it will come out nice.
I have never "made" anything, I just modify the things around me into useful items with abilities that were GIVEN to me.