The problems you listed are one of the reasons why people opt for a Brand new Civic then a few years old import.
These problems are pretty much normal cause most illiterates here use these imports as sports cars and abuse the hell out of them.
Khan motors is a very reputed workshop so I am sure that whatever they did with your suspension will last, they also have a lot of experience in this field. But however if you encounter similar problem again then do pay them another visit.
I would advise you to change the fuel pump, get tuning done and change all the liquids in the car to kinda give it a fresh life.
And if both workshops are assuming that this problem is caused by fuel filter, then i guess that is the culprit.
The "direct exhaust" your friend told you about is actually called a "free flow exhaust". They remove all the dholkis or whatever and make a free flow pipe all the way down the car which gives a nice sound and improves performance a bit. That's a different matter depending upon if you want to increase the factory performance. I don't see how that can fix the main targeted problem as free flow exhaust is like an add on, i don't think it can resolve this issue.
Modifying the exhaust system and adding an air intake will increase your performance but I feel that the problem will still persist, but you will just get a slight gain in performance.
Its normal to have a slightly reduced acceleration when AC is on but definitely not a drastic difference.
You should take the car to a reputed AC mechanic and have him sort out this issue, he'll tell you best if the gas for AC is filled incorrectly or incompletely.
Hope I was of help..