No all stock pipes do not have a baffle. The pipe on the 2.5 does not have one. So you won't need to worry about it. When I removed mine from my Pro .15 I can't say I notice a big difference, maybe slightly better bottom end, and it sounded much better. I was concerned of it melting inside and blocking the exhaust or pressure feed which was my main reason for removing it. I did not use it very long though before buying a new tuned pipe.
Matt, sorry to say it sounds like it may be time for a rebuild, sounds like the piston and sleeve may be worn. Do you know how much fuel has been run through the engine?
What type surface are you running on, grass, dirt, street? If you are running on grass this will cause the engine to run much hotter and puts quite a bit more stress on the engine. Pro .15s will be difficult to start when they are hot. By putting your finger over the exhaust stinger you are actually forcing fuel into the engine, (this is how you prime it with a primerless tank) when the engine is too hot the fuel vaporizes before getting into the engine, this is why its harder to start when its hot. try richening it up a little bit this will help it to run cooler, but not too much to where it loads up and is spitting alot of raw fuel out of your pipe.
Get it to run good before you start modifying it to climb. Then for more bottom end power you can change the gearing, and pipe for relatively low cost. You can also put a spool in the rear diff but you can no longer run it on the street if you do this. Another thing that will help is using a real heavy thick grease in the diffs, this will give you less slip without actually locking the diff.