Reed valves and boost bottles are not needed to make these engines run well.
The chain, the choke, and poor running are small details that need careful attention.
Look at the chain as an example. Why repeated problems?
Was it lined up when you put it on? Was the tensioner on the bottom chain?
Where the bolts tight, but not crushing the tube? These are all details that cannot be missed.
So, when it goes wrong, do you just return it to the way you had it and hope for a better result?
Or do you stop and try to analyze why it failed?
Do you try to put it to the way the manufacturer intended, or modify for improvement?
Modify for improvement is not the first thing you should jump to.
You just bring in new problems without solving the root cause.
So, your running problem.
Understand 100,000s of these engines run well without reeds. You don't need them.
So what then? Let's note your symptoms:
1) oil sitting in carb and filter (this is normal, no worries. I can explain if you want)
2) the longer you ride the less power the motor seems to have
3) if you shut the motor off then later restart, the power is back for a while
4) does not seem to be a heat problem (no reason given)
1) chain problems (solved)
2) Choke sticking on new carb (solved)
3) boost bottle installed with carb, rough running (solved, removed)
4) Tuned pipe/muffler combo (and modified carb) put on with new installation.
This is a case where modifications might be bringing their own problems.
You proved it with the boost bottle and just don't know about the pipe and carb.
Do you think more mods would help? NO WAY. Get back to basics.
As much as possible, return it to the way it was designed and known to run.
Put the stock carb and pipe on it for now (if you have them and they fit) and try it again.
Try one mod at a time starting simple. If it runs stock, try the pipe, if it still runs, try the carb, etc.
If it doesn't run stock, look for detail problems first, noting time as a factor such as blocked fuel flow. So check fuel flow, if it is poor, look at filters, valves, tank outlet, carb inlet.
I hope this helps you solve not only this problem, but any that come up in the future.
Please keep asking and tell us what worked or didn't so we learn too.