I'm going thru the same process right now (although slowly)
Started with uni pods, 127.5 mains and 3 needle shims, MAC 4/1 with baffle, but wanted to go back to stock airbox.
Here's where I am now (attachment)
Will be adding a shim and see from there.
I think sometimes people buy into the need for re-build kits when they really don't need them. I have 42,000 miles on mine with all orig internals except mix screw o-rings and bigger slow jets....and they have been opened up several times.
Which year motorcycle?
What is the thickness of the three shims on each needle?
What idle jets?
Mixture screws set at 
Is it a baffle or a muffler?
Lucky,
I finally found my extra shims and they measure as follows:
0.50mm thickness (after sanding the burrs)
6.75mm OD
3.10mm ID
I think they are simple 3mm washers, but need to be de-burred
I also think the 42 pilot was over doing it from a stock 35.
If you look at the spreadsheet, you will notice that changing any one item, can affect other circuit totals.
The reason I went with the live Dynojet A/F meter was too be able to tune for less than WOT on the road, and get smoother transitions from circuit to circuit. And I was suprised to find how much of the actual riding time the throttle position was very low (1/8 to less than 1/2).
78 CB750K8
PD42B's
Stock airbox drilled (4 1" holes in back of box)
K&N
MAC 4/1 with baffel in muffler
112.5 mains
42 pilots
1 shim (0.5mm) under needles
Mix screws 1 out
2500' elev
65-80F
Still a little rich on top and bottom, and lean in middle, but definitely better than with pods.