A major decision-Replace entire cowl

Today I decided to do the right thing and replace the entire upper and lower cowl. This means that I will have to either return for a refund difference from my parts supplier, or to find a way to sell the cowl repair end panels I previously bought for $45.0 a piece.
I just could not respect myself any more if I left that scrap of rust in my car. It had to go. So I got to work. It took me a couple of hours of spot weld drilling and some chiseling and banging. the upper cowl came out in pieces. The thing had been repaired with sheet metal and rivets, JB Weld and Bondo. The hats were replaced with riveted sheetmetal hats around the rusted-through lower cowl metal. Shame shame!!

  

 I am a bit worried about the challenges ahead, but I know tomorrow I"ll be ready to continue this project.

I was looking at the alternatives from my parts supplier; I can buy both pieces separate; the upper cowl for $187.45 and the lower cowl for $177.15, for a total of about $364.0. or I can buy the entire assembly welded together (e-coated on the inside) for $391.0. To me it seems a no-brainer to buy them welded together, but I am wondering if there any drawbacks other than the painting, that I might be missing by installing the entire assy. together, vs installing them separate. Can I rattle can paint it through the vent openings then restrip and prep the upper cowl and repaint it with the rest of the car? How else can you get the inside of the panels painted if you buy then welded together? 

http://www.cjponyparts.com/cowl-panel-assembly-1-piece-1967-1968/p/COWL4/