You are eligible for day-of-departure comp upgrades to D1 after upgrading to PS with GUCs if there are any open seats left. I would not count on getting any online seat upgrade offers to D1 after applying a GUC to PS on flight (the system also does not really seem to look at which class you are currently booked in to determine pricing as it is quite primitive).

If there are no online seat upgrades available for purchase and you do not wish to try your luck on day of departure, your only option is to refare where you are just paying for fare difference between your original Main fare and D1 fares (Delta will not offer you any kind of discounted upgrades to D1 just because you applied a GUC to get PS seats).

What, specifically, are you using in your multi-city searches? If you are trying to specifiy flights segment-by-segment, that won't work. I was able to use ATL-VCE + KEF-ATL in a multi-city search and it works just fine.