These are the steps to make sure the rig is setup the same as for VRChat Unity package after editing.
((Some Basic Blender knowledge is required in these steps as in combining meshes, running python scirpts, and adjusting material order.))
(((Be sure to export with these settings under Transform inside Blender)))
Scale 1.00,
Apply Scalings (FBX All),
Forward (-Z Forward),
Up (Y Up),
Apply Unit: (checked),
Apply Transform: (not checked.)

Keep and combine the meshes you wish to keep, (may require CAT's plugin or any method of combining meshes together in Blender.)
(Will need to combine otherwise visemes won't work well)
After combining, do the 2 python scripts bellow on the avatar's main combined mesh's.

There be a list after the scripts of order you want to do the materials to try and keep slot order the same
(As far my experience if it ever changed like new material added it just randomly orders and breaks any material swapping animation)
(Just something always struggled to deal with in Unity2019)

If keeping Digi grade option rig, make sure planti boxes are separate so can be hidden easily by deleting mesh rendering in Unity

After ordering the blendshaes and renaming for MMD,
the rest of the steps can be ignored but just in case you want to make sure, I left in the steps I do after exporting from Maya.

(You will still need to check the Ankle rolls as for some reason it keeps flipping that back)
((make sure the roll is correct on the Ankle Joints set correct down bellow whenever empty skin weighted joints are deleted))

Python script 1: found at link: Link to it https://blender.stackexchange.com/questions/149738/how-to-sort-shape-keys-by-a-to-z-in-blender-2-8
ordering Blendshapes by alphabatizing on mesh that is selected:
-------------------------------------------- copy scripts bellow
#start1

import bpy


ob = bpy.context.object
skeys = ob.data.shape_keys.key_blocks 

skey_names = sorted(skeys.keys(), key=lambda v: v.upper())

for name in skey_names:
    idx = skeys.keys().index(name)
    ob.active_shape_key_index = idx
    bpy.ops.object.shape_key_move(type='BOTTOM')



#end of script1:


Python script 2: found at link: https://blender.stackexchange.com/questions/254643/rename-shape-keys-with-python
This Renames the blendshapes of selected mesh to MMD blendshape names but make sure blendshape "Basis" on top first:
(This only works on main mesh with all MMD blendshapes are listed correctly.
The list of them all are bellow as example "MMD10_O_O はちゅ目" as first blendshape.
it simply names from top down so they need to be ordered top of the list and in alphabit.
------------------------------ #copy script bellow:
#start2

import bpy, re
# get the selected object
selected_object = bpy.context.object

# get its shapekeys
shape_keys = selected_object.data.shape_keys.key_blocks

names = ['はちゅ目', 'わぉ?!', 'なごみω', '悲しむ', '敵意', '瞳小', '恐ろしい子！', 'あ', 'あ２', 'え', 'い', 'ん', 'お', 'う', '怒り', '下', 'にこり', '困る', '上', '喜び', '笑い', 'まばたき', 'にっこり', 'ウィンク', 'ウィンク右', 'ｳｨﾝｸ２右', 'ウィンク２', 'なごみ', 'はぅ', 'びっくり', 'じと目']

# loop through shapekeys and replace the names
for index, key in enumerate(shape_keys):
    if key.name != "Basis":
        try: key.name = names[index - 1]
        except: pass



#end of script2:
#
MMD listed blendshapes and translation

MMD10_O_O はちゅ目
MMD11_Waoh わぉ?!
MMD12_Howawa なごみω
MMD13_Wail 悲しむ
MMD14_Hostility 敵意
MMD15_EyeSmall 瞳小
MMD16_EyeFunky 恐ろしい子！
MMD17_Vis_A あ
MMD17_Vis_A2 あ２
MMD17_Vis_E え
MMD17_Vis_I い
MMD17_Vis_N ん (was half of NN blend)
MMD17_Vis_O お
MMD17_Vis_U う
MMD18_Brow_Angrey 怒り
MMD18_Brow_Down 下
MMD18_Brow_Smiley にこり
MMD18_Brow_Trouble 困る
MMD18_Brow_Up 上
MMD1_Joy 喜び
MMD2_BlinkHappy 笑い
MMD3_Blink まばたき
MMD4_MouthSmile にっこり
MMD5_WinkL ウィンク
MMD5_WinkL_Happy ウィンク右
MMD5_WinkR ｳｨﾝｸ２右
MMD5_WinkR_Happy ウィンク２
MMD6_Howawa なごみ
MMD7_EyesSqueeze はぅ
MMD8_HA びっくり
MMD9_JitoEye じと目

Order of Materials in Blender:
BodyMatt
Credits
EyesInnerMatt
EyesOuterMatt
HairMatt
MiscMatt
PropsMisk_Matt
WhiskersMatt

(Rig edits after importing from Maya)
These are my pipeline steps through Blender from Maya.

-Reparent Neck on top of ChestUp

-for Digi parent Ankles to TopFut

-Make sure Toes are rotated correctly in the set rotations saved

Right ankle needs to be rolled 180 (For some reason it flips on that side)

Toes roll angles to straiten orientation:
Rolls:
Right Ankle 180

ToeIndex1_R 10
	ToeIndex2_R 106
ToeMid1_R 178
	ToeMid2_R 180
ToeRing1_R -50
	ToeRing2_R -160
ToePinky1_R -9
	ToePinky2_R -105

ToeIndex1_L -10
	ToeIndex2_L -106
ToeMid1_L -178
	ToeMid2_L -180
ToeRing1_L 50
	ToeRing2_L 160
ToePinky1_L 9
	ToePinky2_L 105

Planti leg Rotations
Rolls:
Right Ankle 105

ToeIndex1_R -12
	ToeIndex2_R 106
ToeMid1_R 178
	ToeMid2_R 180
ToeRing1_R -50
	ToeRing2_R -160
ToePinky1_R 9
	ToePinky2_R -105

Left Ankle -105

ToeIndex1_L 12
	ToeIndex2_L -106
ToeMid1_L -178
	ToeMid2_L -180
ToeRing1_L 50
	ToeRing2_L 160
ToePinky1_L -9
	ToePinky2_L 105