Caveat: I do *not* know how many spots for large foundation pads there are in a basic (wooden wall) guild castle. From foggy memory, I'm going to guess 8 large pads, two on either side of the inner keep, and four in the front half of the courtyard in front of the keep.
Most info on buildings for the castle are here:
http://www.theromwiki.com/Guild_Castles and
http://www.theromwiki.com/Siege_Wars Seem to be relatively up-to-date. Drill Grounds are currently inactive for Siege.
In order to get the better buff buildings, you'll need to have at least a lvl 9 castle.
Buildings needed for siege:
Academy
Library
Stable
Processing Factory
Forge
Field
Lumber Yard
Farm
Throne (inside keep)
My recommendations:
Academy VI and Library V, both required for Stable VI (12% mount speed buff).
Forge VI, Field V (needed for Library V and Stable VI), and Lumber Yard VI, all 3 can fit on one large foundation.
3 Proc Factories, and they don't need to be taken any higher than lvl III--there's no improvement to the items available, their powers, or the number of Crystal Extractors (5) in each Factory.
Farm can stay at lvl I, you won't get any more than 10 Assault or Battle Time scrolls.
Throne is necessary for attack scrolls, but I do not know if there are specific requirements in order to purchase a Throne, other than having a lvl 5 guild and a castle.
If you use the above scheme, you will not have foundation pads for either an Arsenal or Attack/Defense buff towers.
The reason why siege guilds want the stone wall upgrade is for the four additional large foundation pads on the outside of the castle. They can stick buff towers or other buildings on those pads. IMO, that's the *only* reason to go for the wall upgrade, and it's also where the Drill Grounds, Academy, and/or Library can be placed so an additional Proc Factory can be put inside the castle.
YMMV, mine certainly does!