Mickey, the first thing you need to do is put a sealed airbox back on the bike. With stock jetting, it will not run right without a sealed airbox. The open air intake hole in the bottom of the box should measure about 1/2" x 3". Otherwise, the box should be airtight.
To check to see how well your plugs are sparking, remove a spark plug.
Put the plug into the plug wire/cap and ground the plugs threads against an engine cooling fin. While holding it there, touch the starter. (make sure your kill switch is in the on position and your clutch lever is pulled in) If the clutch lever is not pulled in, the interlock will kill the ignition circuit.
You should see a good, blue spark on the tip of the plug electrode.
Check the plugs/wires for all four cylinders. Let me know if you have spark on all four sparkplugs when they are grounded to the engine this way.
Do this check just to humor me if you would please.
Remove the gas tank. (raise seat, remove hold down bolt at rear of tank,
unplug fuel and vacuum lines from petcock.) You will see two coils, one on the left side and one on the right side of the frame. The left coil fires cylinders 1 and 4. The coil on the right side fires cylinders 2 and 3.
The 12 volt positive power feed/supply to each coil will be an orange/white wire. That orange/white wire must go to the terminal on the coil that is marked +/positive. If someone has reversed the polarity of the connections, the bike will run, but it will run like crap.
If you have a multimeter, unplug the wires from the positive and negative terminals on the left coil. Set the multimeter to the lowest ohms scale. That could be X1 or 200 depending on your meter. Connect the red and black meter probes to the + and - coil terminals on the left coil. Any reading between 2 and 5 ohms is within service limits. Average is about 3 to 4 ohms. Make the same check on the right coil.
Let me know what the results are for the two coils. This checks the primary side of the coils.
The secondary side is checked by setting the multimeter to the 200K scale.
You will touch the multimeter probe tips to the metal contact in the spark plug cap. One probe to the #1 spark plug cap contact and the other probe tip to the #4 spark plug cap contact. Resistance should be between 30K-50K ohms. Do the same thing between plug wire #2 and plug wire #3. Let me know what reading you get.
If your primary coil resistance is between 2 and 5 ohms and your secondary resistance is between 30K-50K ohms, then your coils are fine.
If secondary resistance is incorrect, it is probably faulty plug caps.
If you need to replace plug caps, you will need the NGK 5K ohm caps.
A loose baffle in the exhaust will not make any difference other than to annoy you with the noise.

I have on in my 750 too. eh eh
Also, set the multimeter to the 20 volt DC scale and tell me what the voltage is at the battery terminals. Then put the multimeter red probe on the orange/white wire that powers the coil and the meter black probe to ground. With the ignition turned on, check the voltage to the left coil and then to the right coil. Let me know what the voltage level is going to the coils.
We have a frequent poster in the forums that is fond of saying things are never balck and white, they are shades of gray. A bike is like that. Everything has to work together. A bunch of small things, that by themselves would be insignificant, when put together will make it impossible for the bike to run right and sometimes not at all.
Not knowing what the shop checked or what condition anything is in is why I am asking you to do these checks.
To reliably do any kind of carb adjustment, you first must know:
1. voltage available at the battery
2. voltage available in the harness to power the ignition system
3. The condition of the air induction system (intake tubes/airbox tubes and filter)
4. verify ignition timing is correct
5. verify ignition system components are working and to spec's
6. Your bike has points and condensors, (if it is still stock) so you will need to set point gaps and at least static time to the F1 mark for the left side points and F2 mark for the right side pointset. If you need spec's and instructions on how to do this and what you will need, let me know.
If any of these things are wrong/faulty, you can adjust carbs until you turn blue and it will do you no good at all.
I suspect you will find very low input voltage or reverse polarity on your right coil. (just a guess at this point)

Its also probable your ignition timing is off and if it is, then its a sure thing your carb synchronization isnt quite right either.
Lemme know..........
Earl