My home conversion LDV is insulated sides and roof, but only with fibreglass loft insulation, and then lining carpet over the ply/hardboard inner skin. Its not that bad at all for warmth actually, though I have done quite a few things to improve it (the van was part-done as a Moto-X van when I got it, was a budget first van which we now are fond of, so I wasn't about to rip it all apart anyway).
But like you, I had to 'think outside the box' a bit to improve insulation without going nuts with the work or the budget. Here's what I ended up doing....
A lot of cold ingress comes up through the floor as well as escaping through the walls/ceiling - so stopping it getting in there helps overall. So Ive done a bit to tackle that without having to go nuts with the tools (see below) - maybe its worth thinking about for you?
My overcab storage also though had nothing when I got the van - just the thin glassfibre roof. I did cover with camping mat to start, but that didnt seem to do much.
Now I have the double-faced foil insulation stuff they flog in Wickes and the like (and which I used double-thickness to make my Window 'silver-screens' out of which make a big improvement over the windscreen and the cab door windows) - its a sandwich of foil with bubblewrap as the filling, basically. That in turn is covered with cheapo-self-adhesive carpet tiles. Seems to work quite well. (Note, a foil face, facing into the van will improve things, but is also an ideal place to build condensation. I found if you cover the foil face over with a layer of carpet tiles [or indeed lining carpet should work as well, but more fiddly] seems to solve the condensation issue completely).
I also got a hefty roll of the (heavy) thermal insulation underlay from the builders merchants (dense heavy underlay with foil on the upper face) that is intended for putting under house laminate flooring. I had already used flashing tape all over the cab floor (for acoustic reasons), now I have added a layer of this thermal insulation, then reinstated the rubberised acoustic (hah!) floor mat, and then added a thick carpet offcut over that. The cold ingress from the cab floor is now a good bit better, and its a bit quieter.
I also used some of the remaining laminate floor heavy underlay insulation to put inside the bottom of all the kitchen unit cupboards, and also cut sections that sit on top of the floor when the bed base is pulled out. The sofa section is lined with this stuff permanently, while the moveable 'insulation mats' for the rest of the bed floor area sit between the pull-out frame sections for the bed - all to add extra floor insulation while sleeping.
To add to that, even more of this underlay insulation was glued to the bed base sections, and then covered with carpet tiles so that the mattress cushions are well insuated to prevent cold/damp/condensation. All this is to minimise the heat and cold transfer between us on top of the mattress and the cold under the floor by adding layers of insulation between the floor / air gap under the bed / bed base / mattress.
When the bed is put away as a sofa, the extra floor insulation sections are stored underneath the sofa in the base section with the duvet.
As my roof is lined with lining carpet, it allows velcro to be employed. So, I made double-thickness silver screens with velco edges - I stick these over the side door window, and over the skylights to keep the early morning light out, but also they really do help keep warmth IN.
There's lots of my inane ramblings on what's been done to my van on a thread 'Sully the LDV Convoy' if you can stand reading it - but its pretty much what I've summarised above for insulation.
Left-Field, Untried Idea Section
Only other possibly useful trick I can think of for successfully getting a loose insulation such as recycled bottles or beads into the cavity and getting them well distributed.... its a trick I watched a mate doing when shuttering concrete to get trapped air out......
Drill small holes at the top of a section of inner cavity - just enough in each section to be able to pour your insulation media in.
To get the insulation media you choose to settle to the bottom of a cavity section and build up without gaps (bear in mind that if you have horizontal internal wall stud-work then you'll need to treat each lower panel under a strut independently)...you need a
battery drill set on 'Hammer'.
Put a small block of wood against the inner wall face (to prevent marking/damage from the drill chuck) and then put the drill chuck (no bit in it, obviously :lol-053

against the wood block and give it some welly. The hammer action will vibrate the inner panel and get the insulation media to settle and distribute, so that you should get good fill without any missed areas due to trapped air or whatever. Then just keep feeding more media in till it doesn't settle any more, close off the fill hole and do the next panel.
This idea won't help you with the roof so much though, but it might work well for the walls maybe? (Unless of course, guys like nbrown who know lots more than me know different). I don't know if its ever been done, but theoretically it might work as an idea/fix?
You could for the roof simply velcro large sections of 'silver-screen' stuff across the roof at night (a bigger version of what I do over the skylights -the stuff is plenty light enough even double-thickness to stay put with velcro so you can easily take down and store when you don't need it).
Minimising Heat loss through the worst areas - the glass
If you haven't done so, then making inner 'silver-screens' to cover the glass really helps curb heat-loss.
Pretty easy to make... make a template to suit the windscreen etc. out of cardboard or something (with an overlap so the glass is fully covered), then cut out your insulation.
Spray glue 2 pieces together to make a double-thickness screen.
Seal the edges with Foil Adhesive tape - TA-DAAH!
If you want to be posh you can add eyelets and suckers to stick them to the glass like I did (a well-known auction site came up with the goods), but I needn't have bothered for the main swindscreen - simply folding down the sun visors holds it in place nicely. (Fold the screens up in a 'concertina' fashion for storing - look after them and they'll last ages - the ones I knocked up are going strong after over 2 years)
Put a curtain-rail up between the cab and the hab space, and put some heavy full length lined curtains up so you can close off the cab area from your living space. You then have a smaller area to heat, and insulate yourself a lot more from the cab glass heat loss problem.
I hope this helps.
G.