ok, sorry for slow reply, i had a couple of things to do.
nasty place for a problem, i was thinking botton was the problem, ok ....
1) your man is right, if you have a good replacement, then you replace all of it, the one you have there you carefully grind off the welds from the side of the seems not needed, or you use one of those spot weld cutters that cut around the weld and allow you to grind off the leftover later, this will remove the unwanted metal connected to your new panel, then you use a normal drill to drill out the spotwelds in the van (having cut the panel out 10mm inside the seam line all the way around, this will leave you a series of holes to spot weld the replacement panel in with. obviously the top it the oposite way around as you dont want to drill through the rain channel (see below for a reason why you might have to)
for the bottom simply drill through the spot welds on the van and weld the new panel on through the holes from the rear
then line up the replacement panel and weld it in using the holes you drilled to remove the original welds and any extra ones you find you need to add, seal it all up with grey stripe sealant and away you go.
2) if your replacement panel is not good, and cant be straightened to a point you are happy with then you are left with no choice but to replace the bit your not happy with on the new panel, in this case the bottom, and join it at a point that is not flat, ie that swage line ...... question, what is wrong with the bottom on your van ? if nothing, then no point in removing it, only to replace it .... more work than its worth
so, working on the principle that the bottom on your van is good, then you need to decide where to cut it, normally i would be tempted to say go to the lower swage line as it is a smaller section than the upper one and less likely to warp when you weld it, but looking at your replacement panel, i would go for the top one in this case,
3) Take the glass out at this stage as it will prove easier to work with it removed
4) i would be looking to cut your van along the line above the side repeater in the picture (it looks missaligned anyway

), at the top of the reccessed piece, cutting off the bend that brings the panel back out from the van, so that looking in profile (from the side) the panel comes up, bends back in towards the van and then bends back to vertical then stops just short of the bend back out (and i do mean close to that bend, not 5mm below it) infact i would be tempted to cut on that bend or maybe even a couple of mm after it, allowing for the thickness of your cutting tool, remember you can always skim a bit off but cant put it back so easy, to cut this you need something that will cut a straight line or close (although this can be straightened later if you errr on the side of caution and leave a little of the bend) an airsaw would be ok, but might be hard to keep straight and also if it catches in the metal it will bend it, a nibbler will not get in tight enough, a 12 inch grinder is just too big, so i would go for a 4 1/2 or 5 inch grinder with a very very thin stainless steel cutting disc (1mm or less) this would be a good compromise, and cut as close to the edges as i can without cutting the frame, and finish it off with a thin hacksaw blade, you might find this actually easier to cut from the inside, especially if your not too steady with the grinder or dislike workigng at odd angles, wear a good set of goggles and face protection and then you can get quite close to it while you are cutting and see better, i use a full facemask with a filter on it from 'Sabre' ... very good
i cant stress how much cleaner a cut you will get with one of these thin stainless steel cutting discs, 100% better than normal cutting discs in my opinion.
5) ok, now cut all the way up the sides to the top 10mm inside the seam line,
that should leave you just the top section left connected
6) cut from the top left of the window frame, up at an angle to the top of your vertical cut on the left, repeat the process on the right, this will remove the bulk of your panel, leaving only the section above the window connected (much easier to work with)
7) now cut 10mm below the rain chanel, all the way from one side to the other, you will now have much easier access to the joints you need to remove.

examine your new panel for how the top section is constructed, i havnt looked too closely at one of your type, but on the mk2 the roof is one panel and actually stops at the outer edge of the rain channel, the section below this (that it is welded to) goes through into the van and forms the C section channel that runs around the top of the van, the side panel folds back at the top by 90 degrees, and is spot welded to the lip on the edge of that C section around the top of your van, producing a 3 layer sandwich along the line of the rain channel, now you have to decide how you are going to re-attach the panel once you have the old one out,
if you opt to remove the leftover edge of the old panel cleanly, then cut or grind the welds as before and drill the top of your replacement panel .... BUT, and here is the problem, you are going to have to mig weld the panel back in place, and you need to make sure you can actually get up there to weld it

..... so the other option (and the one i would go for, mainly because i know i can do it) is to remove the unwanted metal sections on the top of your new panel cleanly leaving no holes in it, then drill out the welds holding the edge of the old panel to the van, drilling all the way through the rain channel :O (if as i suspect, and there is weld through sealant between these panels, then a small pencil blow tourch will be usefull later to burn it out from around the holes so as not to contaminate your weld)
9) now for the sides, and this i am going to be working blind on as you cant get any pictures, but if i am not mistaken, at the joint of each of these side panels, there is not only the lip of each side panel, but also a strengthening rib, so again you are working with 3 thicknesses of metal ... typical ford and a real pain at times, especially if the one you want to remove is sandwiched between the other 2
i will stop there for now as it is hard to consider the best move to make next without seeing the construction of the side panel joints, can you get a shot of the inside of the 'new' panel. showing the joint ??
hope this lot was at least a little help