There's several different techniques to use and I'm not the last word on this either. May I begin by asking why the punches are so very long? Any good design will use as short a punch as possible to avoid the potential misalignment over a longer length. Even if your part has large "Z" depths to it a shorter punch can be mounted (where possible) on a block to make up the difference in Z. I've only had the occasional punch exceed 3-4 inches in length. Any punch longer than 6" is a candidate for examining the die design.
Most dies I've built I pinned the punch plate last. Transfer screws, 1/64 under dowel size drills, and careful checking of clearance alignment between every operation is critical. How you ensure the alignment of punch to die section is also quite important IMO.
How long are your punches that a standard drill length won't reach? There are smaller drill chucks, I've also made drill/tool holders for extra reach. If you've spotted the location of a punch plate/holder then you don't need to leave it mounted to perform the full depth of the hole. Once you established the hole location (3-4 times the hole diameter for example) then leaving the punch in place to do the rest of the drilling/reaming/tapping runs the risk of damage occuring. I always just spotted the location, removed the punch, and then finished the operation. Initial reaming of dowel holes was done with an undersize reamer with the punch plate mounted and then final size (.0005) with it removed to avoid changing the reamer size (hardened punch holder) or the hole size (soft plate).
The above is for dies with .003+ clearance per side, less than that and the % of misalignment begins to greatly affect the results. For those sort of clearances a radial drill press can be used for lots of the hole work. For clearances of less than .002 per side there should be other machine/assembly methods to ensure accurate locations. Even the die components will change per the tolerances of the operation (box stripper vs. spring type for example)
My point here is that every die has it's own requirements that dictate the machines used, the assembly methods, and alignment procedures. I'm not trying to be vague here, just noting that every job is somewhat unique. More info about your work, material, die design, etc. will probably net more info from the crowd.