My favorite rod for flipping is an older AllStar that I've been using for ten years or so.  I need one more project to get me through the winter, so I decided to strip the guides off and replace them with titanium nitride guides. I'll only be using the rod for flipping and the occasional short pitch. Could I do an acid wrap placing the guides in the same positions as the ones I removed, or am I better off going with the original configuration?

I don't see an issue.  Put the srtipper guide at 0°, the next at 180° and put a bumper at 90° halfway between them.  Place the runners on the bottom and static test it.  Youll know then if it'll work.

Thanks

I did a rewrap on an couple Allstars last summer . The spacing wasn't too bad but I didn't follow it exactly. Lightening the guide train did wonders for the rods. 

The problem with changing the spacing is that it is (for me, at least)  impossible to finish off the old guide positions and to have a decent looking rod, the whole rod will most likely have to be refinished.  If the old positions are about right, keep them, even with different guides.  If you do a simple spiral the 90 degree guide will be an added guide between #1 and #2, so will not introduce any finish problems.  

The simple spiral positions all guides the same as conventional exc that your second guide and all others to the tip will be at 180 degrees.  An added guide, placed at 90 degrees, is positioned half way between #1 and #2, and its only function is to keep the line off the rod.  It will have no torque on it, will be loaded directly toward the blank, so it's not under high stress.  Make it the same diameter as your running guides.  (all guides can be the same, small, size, exc #1 which needs be no bigger than a  6.  Think Fuji reverse KR (single foot facing the reel).