To answer your first question yes. To change pumps you will need the inline pump, drive gear, new timing case housing, pump support bracket, oil feed line to the pump, new injection lines, injectors, new lift pump and possibly pistons. It would not be termed a cheap conversion. I mentioned the pistons because inline engine generally have different combustion bowls in the piston but the others have been used ok.
As for which is better, it depends on where you're going with the engine. The VE rotary pump was used on about 95% of all the road use 4bt's. It is a fairly simple pump and replacing seals is not a major affair. It can be modified to produce a lot of power for not too much cash outlay. Adjusting the pump timing is not too difficult and as you noted you have all kinds of screws to adjust and tweek to your heart's content. The inline pump on the other hand has none the screws. Fuel metering is handled by the pump but there are mods that can be made. For more fuel you can change the delivery valves or adjust or change the cam plate in the pump. Inline pumps were available on 4bts in several types and models. There were "A" pumps found on industrial engines as well as P3000 pumps. The gold standard of the inlines is the P7100. That's the one everyone wants. These can be tuned for extreme performance. The P pump generally has the best reliability history and can deliver better fuel economy, but it comes at a cost. I have seen new VE pumps for sale in the $700-1000 range. If you bought a new P7100 you'd be looking at 3 times that amount. Just recently there were 2 Cummins rebuilt P7100's sold on ebay and they went for about $1600 each which I thought was quite reasonable. There was a P7100 take off complete with all the accessories except injectors which brought about $2000. That was getting close to what some like to pay for a complete 4bt. If you ran down to the local Cummins store and gave them the list of parts for a complete change over you'd probably be staring at $5000 worth that you could carry out in your two hands. Most of the guys who build really high performance engines go the P pump route but there's nothing wrong with the VE.