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I'm currently using a KR Multicase with re-purposed 40k Eldar foam trays for carrying my Flames stuff around in, but seeing as how my collection is growing rather rapidly and the dimensions on some things aren't exactly perfect for 28mm trays, I've been looking into getting a case and some trays purely for FoW stuff. Most people I know use Battlefoam and their pre-cut range of FoW trays, but being hopeless with sizes and exceedingly paranoid about ordering the wrong thing--especially expensive 'wrong things'--I'm really unsure about which trays would work for me in what combinations.

Currently, the only armies I plan to use are:
EW Czech Panzers - Dual 38(t) HQ, 2x 4 38(t)s, 1x 5 II Cs, 2-4x 8-rads, 4x sd kfz 10/5s, Stuka.
EW Gebirgsjager - HQ Platoon w/ 2x MG34s, Maximum 2x Full Gebirgs platoons (incl. mortar and cmd), 4x GW34 mortars (incl. cmd + observer team), maximum 1x full pioneer platoon (incl. cmd), 3x 5cm PaKs (+cmd), 4x 3.7cm PaKs (+cmd), 2x 8-rads, 4x sd kfz 10/5s, Stuka.
MW Fallschirmjager - HQ Platoon w/ 1 Sniper, 2x Full Fallschirm platoons, 1x Short Fallschirm platoon, 2x Recoilless guns (+cmd), 3x Marder III (7.62cm), 3x 5cm PaKs (+cmd), 3x NW41s (+cmd, obs, kubel), 4x FlaK38s (+cmd).
LW Soviet Guards Tankovy - 20x T-34/85, 3x DShK Trucks (+AA bases), 3x SU-100s, Sapper Company w/ 2 Platoons (+cmd), Short Spets (+cmd, HTs).

I don't want to store all of them in the same case at once, but some level of multi-purpose would be preferred. I only use armour in LW currently, so my Brits aren't listed because the Tankovy requirements are pretty much exactly what my Brits need + more space (excepting, perhaps, room for 4 25pdrs/heavy mortars). Currently, my Czech Panzers fit neatly into a single old Eldar tray, with the exception of the Stuka and the 10/5s, so they're not a huge issue, but the infantry forces don't really fit anywhere, and with some of the guns protruding off the base at the short side, I'm not sure how to fit 7 PaKs into any of the Battlefoam trays, nor where to put the (Zvesda) Stuka.

The amount of options and measurements is a little confusing, and I can't help just zoning out when trying to make sense of them, so any help or advice pertaining to how to pick trays/cases would be a huge help. Cheers.

check about the website http://us.battlefoam.com/categories/Flames-of-War-Bag-and-Foam-Trays/
they have special trays

I know they do--I even acknowledged it in my post. I maybe rambled a bit and wasn't clear. I don't know which of the trays on offer, and in what combinations, would be the best for the job. Like I said for the PaKs for example, some of the guns overhang, and I don't know how much clearance a medium base slot gives for that. The amount of options, the number of different layouts, and the varying measurements, are too confusing for me.

A year back I luckily won and army and it came in a KR case which was perfect and it's still serving well.

I have also stored troops in plastic clear really useful cases with KR trays in them and they work really well