99 chevy tracker is running very rough, hard to accelerate

you need to let the RPMs drop down to match the speed you're going for the next gear, though this is less efficient than power shifting through.
Unless you're slipping the clutch to smooth out the gear change, yes, there will be a definite surge every time you grab a gear in a manual transmission vehicle. Most automatics will also shift noticeably harder at WOT.
For more sedate, "normal" driving, you can shift slower and feather the throttle a bit more to smooth out the gear changes, but when you're ******* the throttle as soon as the clutch engages, it's going to be a firm shift. I hope is ok.

You have a broken part inside the transmission, it will need to be torn down and inspected.

try adding brake oil to the resvore on the drivers side fire wall first !But if it is out r&r on your transmision is about 385.00 plus parts

Hi Seth, Check out your engine and gear box mountings! Regards John

Have you checked the fuel pressure under a load, low pressure will cause these symptoms. The test port is on the top of the engine in the fuel supply rail to the fuel injectors, the fuel pressure test port looks like a large tire fill valve. You will need a fuel pressure test gauge to do this test (about $20), the pressure must be watched while you accelerate, it should never go down on hard acceleration just up about 6-8 PSI

need more info need to scan and post the codes pulled

u need to have the system tested for trouble codes, but u most likely have a defective trans 1-2 shift solenoid. to replace this u will need to pull the trans pan off the solenoids are attached to the valve body, also check the trans connector for water or corrosion.

Sounds like a bad countershaft bearing. The trans will need removed and disassembled to fix it.

yes both of these items can cause your problems

The run rough problem is due a cyl.mis firing,it becaused buy a bad plug,plug wire,coil,or even the ing.module. the servive eng.light flashing is warning you that you have a cyl.misfire that can cause damaget to your catltic converter if you continue to drive it.with may lead to why you think you have a exhaust problem,it may be colgged.