The capped line was probably a pressure side cleaner line at one time. They may have capped it off because it was leaking so if you want to make that active again, I would pressure test the line first to make sure there isn't a leak.

It looks like whomever plumbed the heater took some short cuts. You could fix this pretty easily by dropping the 3-way valve to the same the level as the heater exit so you could eliminate a 90 and the coupler but you would probably need a new 3-way valve to upsize the branch line. This could be a future project at some point since it is completely independent of the pump and I would only redo it if you plan on plumbing in the cleaner line.

As for the pump, the replumb should be fairly simple and you have enough line after the suction side 3-way so you shouldn't need to touch that. Just make sure you use at least 2" line on the pressure side, replace all the pipe from the pump to the filter, and it looks like the suction side may be 2.5" so carry that through the suction side if possible.

Also, do you have a spa? That would change the two speed choice if you decide to go that route. Otherwise the Intelliflo would handle that fairly well.