Julia, 613569 bytes, Loader's Number
r,/,a=0,div,0;¬x=x/2;r<s=r?s:0;y\\x=y0;y\x=y-~y<<x;Z(x)=global~y<<x;+x=global r=(x%2!=0)<1+Z<1+(¬x+¬x);!x=¬x>>Zx=¬x>>+x;√x=S(4,13,-4,x);S(v,y,c,t)=(!t;f=x=r;f!=2?f>2?f!=v?t-(f>v)%2*c:y:f\\f\(S(v,y,c,!x)\\S\S(v+2,t=S(4,13,-4,y)t=√y,c,Z(x)+x)):S(v,y,c,!x)\$S(v,y,c,Z(x)));y\$x=$S(v,y,c,+x));y$x=!y!=1?5<<y\\x5<<y\x:S(4,x,4,Z(r)+r);D(x)=(c=0;t=7;u=14;while(x!=0&&D(x-1);(x=¬x)%2!=0)d=!!D(x);f=!r;x=!r;c==r<((!u!=0||!r!=f||(x=¬x)%2!=0)<(u=S(4,d,4,r);t=t\$d;t=t$d);(¬f&;¬f&(x=¬x)%2!=0)<(c=d\\c;t=S(4,13,-4,t);u=S=0<(4,13,-4,u)c=d\c;t=√t;u=√u));(c!=0&&(x=¬x)%2!=0)<(t=((~u&2|(x=¬x)%2!=0)<(u=1<<(!c\\uc\u)))\\\(!c\\tc\t);c=r);(¬u&;¬u&(x=¬x)%2!=0)<(c=t\\c;u=S=0<(4,13,-4,t);t=9c=t\c;u=√t;t=9)end;global a=(t\\t\(u\\u\(x\\cx\c)))\\a\a);D(D(D(D(D(BigInt(99))))))
r,/,a=0,div,0;
#Convenience operators
¬x=x/2;
r<s=r?s:0;
#P(y,x) in the original
y\x=y-~y<<x;
Z(x)=global+x=global r=(x%2!=0)<1+Z<1+(¬x+¬x);
#L(x) in the original
!x=¬x>>Zx=¬x>>+x;
√x=S(4,13,-4,x);
S(v,y,c,t)=(
!t;
f=x=r;
f!=2?
f>2?
f!=v?
t-(f>v)%2*c
:y
:f\(S(v,y,c,!x)\S(v+2,t=S(4,13,-4,y)t=√y,c,Z(x)+x))
:S(v,y,c,!x)$S(v,y,c,Z(x)+x)
);
#A(y,x) in the original
y$x=!y!=1?5<<y\x:S(4,x,4,Z(r)+r);
D(x)=(
c=0;
t=7;
u=14;
while(x!=0&&D(x-1);(x=¬x)%2!=0)
d=!!D(x);
f=!r;
x=!r;
c==r<(
(!u!=0||!r!=f||(x=¬x)%2!=0)<(
u=S(4,d,4,r);
t=t$d
);
(¬f&(x=¬x)%2!=0)<=0<(
c=d\c;
t=S(4,13,-4,t);t=√t;
u=S(4,13,-4,u)u=√u
)
);
(c!=0&&(x=¬x)%2!=0)<(
t=((~u&2|(x=¬x)%2!=0)<(u=1<<(!c\u)))\(!c\t);
c=r
);
(¬u&(x=¬x)%2!=0)<=0<(
c=t\c;u=S(4,13,-4,t);t=9c=t\c;
u=√t;
t=9
)
end;
global a=(t\(u\(x\c)))\a
);
D(D(D(D(D(BigInt(99))))))
Note that this is longer than it used to; this isNo previous counts because of changes to ensure correctnessI made way too many byte miscounts in the aggressive golfing I've done.