The paper patch experts hang out at the Shiloh Sharps and Historic Shooting sites. Some experts (and a few talented amateurs) also post on the Paper Patch forums on the Cast Boolits Site. Perusal of their back pages will save you time and powder getting set up.

The only .40 I have is a .40-3-1/4 SS, which has thus far resisted all efforts to get shooting well with paper patch.  (Embarrassingly, it shoots better with smokeless powder and grease grooves.) I have gotten good results with two Shiloh Sharps .45-70s and one in .44-77, and a rebored Highwall in.38-55.  For what it’s worth, here’s what I’ve found:

A little bit of windage between bullet and bore doesn’t seem to matter that much.  Bullets for the .45s from 0.441” to 0.443”, patched with tracing or vellum paper from 0.0013” to 0.0022” seem to work OK.  Measure thickness with a micrometer, turning the thimble down hard. Fatter bullets and thinner papers are better, probably, but one must use the mold diameters one gets.  I get better results with the thin paper, regardless.  I wrap bullets dry, with a clear spot at the bullet base; no tail or twist. Bullets of heavier weights (for the rifling twist) work better than lighter ones.  I don’t size after patching, but many do.  No patch treatment or grease cookie.

The bore must be absolutely clean and dry for each shot.  A good bore pig with a dry patch, or multiple wet-and-dry patches until only a light gray color shows on the last means that you are ready to shoot.

Bullet temper is important.  It has to be soft enough to upset into the grooves, but hard enough so the nose doesn’t slump to one side or the other while this happens.  Exotic nose shapes complicate this; best start with old styles.  16:1 is a good start; a hardness tester is better.  Between 8 and 12 BHN works best for me.  Softer gives a core group with flyers; too hard is all flyers.

When in doubt, add more powder.  My straight cases prefer Swiss, 1F or 1-1/2F; the .44 bottleneck likes OE 1F.  Best .45 loads are a case full of powder (~80gr); the .44 likes either 80 or 90gr.  Wads I use are 1/16” or 1/8” cork.  Compression to ~1/8” below the shell mouth, the bullet seated, and a homemade mouth reducer die to “squinch” the mouth just enough so the round can be handled. Avoid roll crimps. My Lyman neck size die is too big for patched bullets.

You may have a barrel that just doesn’t like paper patched.  Besides the .40, I also have a .45-100 that doesn’t, so far.  But I ain’t giving up!

Get I sizer die for your over bore size PP bullets.  In my 40 & 45's I like the patched bullet to be sized to bore diameter.
e.g. my 45-70 has a .450 bore diameter and I size my patched bullets to 0.4503.   
I wipe because I am a target shooter, so a snug fit in the barrel is not a problem to chamber the cartridge.

Keep on hav'n fun!
MikeT

I've never been completely satisfied with the 9 lb paper for consistent accuracy.
One thing when shooting patched to bore or just under the wad stack under the bullet becomes somewhat critical, the powder charge also needs to go up 2-4 grains over what you may of found good accuracy with shooting a greaser of the same weight.
Bullet patched to somewhere between bore and groove diameter usually but not always get by pretty good with the same powder charge as you used with a greaser.
You will seldom find consistent accuracy if the paper thickness is greater than the groove depth.