I've done a couple of windows on mine. I used seal from Claytonrite, sold by Sealsdirect. You measure the thickness of the metal panel, and the thickness of the glass, and estimate the gap between glass and metal. The accepted technique seems to be fit the seal to the van, with the join at the bottom, and with the seal being about an inch too long so you have to force it apart to butt it. Use strips of masking tape to hold in place on the top sections. The offer up the glass, fitting the bottom edge in first, and working the seal onto the sides and then the top. I think i used a metal tool rather than plastic, and came to no grief. Because I used seal with a central strip that was fitted at the end of the process I had bought the appropriate tool for that, and I think that's what I used to work the seal onto the glass. I also had a teenage son to help (and it was he who helpfully suggested fitting it bottom edge first, after several near disasters

), When fitting the central strip, the use of a wet soapy cloth helped immeasurably. I also used plenty of sealant (Arbomast Autograde, never sets, so never cracks), as my windows, like yours, are an imperfect fit. I think I must have found helpful instructions on here somewhere for fitting windows, and there are probably youtubes too. The string technique works for windscreens (very well, done it three times, each time with more and more sealant!)
My windows are now all leak free I think, but I still have copious amounts of rust left on the inside where water has pi55ed in previously.
Hope you get on ok.