these engines will never run better using pod air filters, unless you have a deep understanding of jetting and a test rig.
Reinstate the airbox.
Replace the stock airfilter - if neccesary replace the old paper part with some air filter foam.
Clean the carb.
filter the petrol
balance the carbs
set the valves to the manual recomendations - but tend towards the bigger gap size. on a cold engine.
inlet gap (0.14 to) 0.19mm
exhaust gap ((0.21 to) 0.26mm
check that the wiring is good and well connected - clean the bullet connectors.
check that coil is offering resistance.
set points gap manually to begin with - again go wide.
points gap (0.3 to) 0.4mm
now check timing - best done with a strobe at low revs (check higher revs too to see that advance/retard mech is performing)
Then reset points gap with a dwell meter.
chances are dwell will have you opening points gap wider than the advised gap.
remember this is an old bike with a worn engine - it will perform better with slightly advanced ignition timing at tickover, and with a generous amount of slack on the valves.
spark plug get new ones, they are cheap and worth it.
again set to widest (if you have set dwell to the longest range and cleaned your contacts the spark will be long bright and strong enough to cope, and the fuel air mixture wont stand a chance).
spark plug gap (0.6 to) 0.7mm
a lot of problems are caused by the recent(ish) addition of ethanol to petrol - and most people blame the mechanics of the bike on them. Ethanol is hydroscopic - it attracts water, the dew that forms inside your tank every morning. Ethanol in petrol absorbs the water and does a thing called phase separation - this is when it effectively turns into vaseline (petroleum jelly) and sinks to the bottom of the tank, and the carbs.
It is this gunge that causes any bike that has been standing for a few days to misbehave, with symptoms of blocked jets that could be misconstrued as weak spark or any other classic starting issue.
There are two solutions - 1 keep your bike in a warm low humidity environment, like your living room, or 2 use a petrol stabiliser, wurth and redex both make good products. Simply using a synthetic lead replacement additive is not enough, make sure that the product says that it deals with ethanol.
actually there is a third option, get to your nearest airfield and fill up with 100LL - it is the same leaded petrol without ethanol that these engines were designed to run on.
These engines were designed to produce peak power with a particular setup. air was restricted, exhaust was baffled to produce a designed flow. opening up flow through carbs and exhausts may seem to have a logic, after all bigger has to be better doesnt it? maybe put bigger wheels on it too.. Consider restricting your exhaust to approximate the original system and you will get the power that the original designers managed to wring from this particular engine. If more air and straight through exhausts gave more they would have done it too.