Before you go moving everything.
The master carb is the one with the TPS on, No 4 cylinder, this carb can't be adjusted the others are brought into balance with it. The TPS has tamper proof screws for a reason, it's set to No 4 which is datum, in other words you're not supposed to move it! The Yam manual like all Jap manufactures manuals is not that well written and from a stand point of the person using it has already been trained on the bike on a factor course and is qualified. Now I'm not saying you're not capable or even possible not qualified, far from it. But few have both boxes ticked of the previously stated, if you have you wouldn't be asking the questions
Haynes well lest said better but they're better than nothing 
No4 must be pulling between 230 - 250mmHG (as should all the others) with the idle set at 1150- 1250rpm. Carb tune are pretty accurate but unless they've been calibrated there's no way of knowing. I see many a bike where the owners tell me they've balanced the carbs or dealer/other Mech has, only they're not as most don't calibrate and/or use crap equipment. If No4 isn't pulling the above you need to start looking at firstly the mixture screw front bottom of the carb, this should be 2 turns out same applies to all the other carbs, once balanced. If you can't get it to pull the correct Hg with the screw at 2 turns out or very close each way, you need to start looking for dirty air screws and/or bleed passages. The other very common possibility is were the carbs have been rebuild with crap pattern/aftermarket parts, many just replace jets, needles etc when they don't need to.
No pattern/aftermarket part is going to be as good as OE, that's mainly why they cost more! And why change them if there's no need just a waste of money.
When balancing get the engine warm is you can. Start with bringing No 3 to match 4, then bring 1 & 2 into line, you may have to increase the idle speed depending how far out they are, then bring the two pairs 1- 2, 3-4 into line again you may have to adjust the idle speed.
Once you've got them all pulling within the range they're balanced and the idle speed is correct, then check the TPS it should read 5000. If its not and the Hg, balance and idle are correct then and only then move the TPS.
The chances of you TPS not being moved by now is unlikely, mainly because people don't understand it's a datum and start moving it with the crabs not set correctly as outlined above or it's been replaced (very common) with out checking all the specs, correcting any that are wrong before fitting the replacement.
Setting up carbs isn't easy at times as it's made out to be. Everything depends on who's been there before you and what damaged, crap part/s have been installed and what tools used. Like everything in life it's easy when you know how, many on forums will tell you it's easy, it is but more often than not they're are doing wrong!
Cam chain noise is often out of balance carbs and/or the tensioner between teeth. Providing it's not rattling loudly, get it warmed up and give the bike some stick in the lower gears to the red line for say a days riding out, to should pop the tensioner to the next tooth. If that doesn't work and you've got all the carbs balanced take out the tensioner and set it.
These engines love to rev and they have very reliable cam chains and tensioners.
The master carb is the one with the TPS on, No 4 cylinder, this carb can't be adjusted the others are brought into balance with it. The TPS has tamper proof screws for a reason, it's set to No 4 which is datum, in other words you're not supposed to move it! The Yam manual like all Jap manufactures manuals is not that well written and from a stand point of the person using it has already been trained on the bike on a factor course and is qualified. Now I'm not saying you're not capable or even possible not qualified, far from it. But few have both boxes ticked of the previously stated, if you have you wouldn't be asking the questions
Haynes well lest said better but they're better than nothing No4 must be pulling between 230 - 250mmHG (as should all the others) with the idle set at 1150- 1250rpm. Carb tune are pretty accurate but unless they've been calibrated there's no way of knowing. I see many a bike where the owners tell me they've balanced the carbs or dealer/other Mech has, only they're not as most don't calibrate and/or use crap equipment. If No4 isn't pulling the above you need to start looking at firstly the mixture screw front bottom of the carb, this should be 2 turns out same applies to all the other carbs, once balanced. If you can't get it to pull the correct Hg with the screw at 2 turns out or very close each way, you need to start looking for dirty air screws and/or bleed passages. The other very common possibility is were the carbs have been rebuild with crap pattern/aftermarket parts, many just replace jets, needles etc when they don't need to.
No pattern/aftermarket part is going to be as good as OE, that's mainly why they cost more! And why change them if there's no need just a waste of money.
When balancing get the engine warm is you can. Start with bringing No 3 to match 4, then bring 1 & 2 into line, you may have to increase the idle speed depending how far out they are, then bring the two pairs 1- 2, 3-4 into line again you may have to adjust the idle speed.
Once you've got them all pulling within the range they're balanced and the idle speed is correct, then check the TPS it should read 5000. If its not and the Hg, balance and idle are correct then and only then move the TPS.
The chances of you TPS not being moved by now is unlikely, mainly because people don't understand it's a datum and start moving it with the crabs not set correctly as outlined above or it's been replaced (very common) with out checking all the specs, correcting any that are wrong before fitting the replacement.
Setting up carbs isn't easy at times as it's made out to be. Everything depends on who's been there before you and what damaged, crap part/s have been installed and what tools used. Like everything in life it's easy when you know how, many on forums will tell you it's easy, it is but more often than not they're are doing wrong!
Cam chain noise is often out of balance carbs and/or the tensioner between teeth. Providing it's not rattling loudly, get it warmed up and give the bike some stick in the lower gears to the red line for say a days riding out, to should pop the tensioner to the next tooth. If that doesn't work and you've got all the carbs balanced take out the tensioner and set it.
These engines love to rev and they have very reliable cam chains and tensioners.
Later