JJprise... Assemble, Fill, then Paint?

I have a question that I have been trying to figure out. I am working on a JJprise by Revelle and I looking to use the paint masks from Orbital Drydock to do at least 1-2 color-shifting colors. I have gotten to starting the Engineering hull and am stumped on what to do first.
The real problem is that I would like to fill in the seams on the back spine and a few other places where it really needs it. But the instructions say paint it, then assemble it. The instructions make no mention of using putty to fill anything in. If I paint both main pieces and then assemble them. I wont be able to fill in the gaps unless I sand away the paint or go over the top of it and then re-paint over the entire thing. Both of these options will probably leave terrible results. If I assemble it then putty it then paint it I would have a much larger piece to deal with and then there is the question of when and how to put in the clear window pieces. If they go in ahead of time Ill have to carefully mask them and hope I dont get any underspray...
You can see that Im very confused as to what order to do this all in. I would "like" to use the window pieces and I would "like" to be able to fill in the bad seams. But I want to be able to do a nice paint job at the same time. I have seen a couple of threads with people doing a JJprise but they either dont do any seam filling or they arent doing the aztecking with the masks...
Can someone help me out?

Most folks are building the model & painting in sections. Such as Saucer, Nacelle, E-hull. Build each section out, fill the seams, paint, final assemble, touch up, decals.
Install the window, if you use them. Then when you're doing the seams, mask off everything except the seam you're working on. That way you wont have to worry about masking the windows yet.
If you use my mask set, they contain full sets of masks for all of the clear parts & windows.
Also don't try to paint an entire section at once, break it up so it doesn't seem like there's as much to work with.

The instructions are useful for understanding which bits need to go where, and if there are any assembly steps that must happen before others, but after that it's really up to you.

For mine, I'm taking the approach of assembling the saucer and the rest of the ship as two big sub-assemblies, and then painting from there. This makes manuvering and masking somewhat easier than if the ship was complete, and all the bits that need to be filled and blended together are assembled and can be filled and sanded before paint.

Orbital Drydock said:

Also don't try to paint an entire section at once, break it up so it doesn't seem like there's as much to work with.

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This is great advice - even on my big e-hull and nacelle sub-assembly I've broken it into sections. I'd also happily endorse the Orbital Drydock mask set, it's been a life saver. Quite apart from the aztek and hull plating masks, the thought of masking all those windows without pre-cut masks gives me the heebie-jeebies.

Yep, I have the masks from Orbital Drydock. And they look fantastic. I was just getting stumped as whether I should assemble the engineering hull completly and then fill then paint? Or if I should paint the pieces then glue together and then try to sand the areas where its gonna need some filler and then repaint over and try to blend...
Im very particular about trying to do a very clean job and didnt want to get to far along and realize I should have filled first or last or whatever...

Yep, so I assembled the whole engineering hull, including the nacelles, before filling and painting. You could also do it without adding the nacelles, but you'll want to add the piece between the pylons, since it'll need some filling and the pattern from the masks goes over the seams at that part.

Checksum said:

Yep, I have the masks from Orbital Drydock. And they look fantastic. I was just getting stumped as whether I should assemble the engineering hull completly and then fill then paint? Or if I should paint the pieces then glue together and then try to sand the areas where its gonna need some filler and then repaint over and try to blend...
Im very particular about trying to do a very clean job and didnt want to get to far along and realize I should have filled first or last or whatever...

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Are there any "panel lines" you can use as cut-lines for your painting and masking? For example, if the dorsal spine joint on the 'engineering hull' has panels running parallel to it, you could mask off from the lines to the edge, paint the major parts, install the windows, then assemble the halves, mask off the already painted portions then commence finishing work on the joint seam.

Just make certain your masking materials are compatible with the paint system your are using and your surface prep is good enough to resist any lift off since your tape edges will need to be good and tight to prevent leaks & give clean lines. I recommend running a 'paint pig' test first to ensure everything works as it should. And as always, work clean (as in wash the parts with a mild detergent to remove mold release, give super smooth surfaces a Scotch-Brite pad scrub for some "tooth", clean before painting and keep dust off your painted surfaces.)

Regards, Robert