Yea, I'm not 100% sure if that's good or not lol. I think inside it's still liquid acid like a flooded acid battery, it's just sealed so when charging it doesn't vent. That also means it can't be over charged to balance the cells like a flooded acid battery (shorter usable life I'd guess). A quick google search suggests mounting it an an angle is fine, but upside down is a no go so based on that sounds like it should be fine. The battery type I was thinking was needed for the angle was a AGM battery since the acid is absorbed into a glass mat.
One perk of low mounted batteries is lower center of gravity, should make handling on cement a tiny bit better (probably near unmeasureable though lol).
Also read up a bit on how 2 stroke exhausts work since you're fabbing your own exhaust system. I'm not sure if there's an online calculator or anything, but pipe size and length are pretty critical to have a good running engine. Since it's likely to be putting around, going OEM sized or even smaller would be ideal for low end torque I'd think. Large around pipes are for more HP, or high rpm power generally. Going too big isn't good either. Think about it, a small car engine can run with a 1.25in exhaust making 75hp+, how big of a pipe does a ~13hp engine need. Also don't run an exhaust tip that flares out, it acts like a megaphone. I'm not sure how much pipe size effects noise. For the muffler, from memory, the tractor pipes are straight though with packing around the pipe and small holes. In the car world I'm pretty sure they are called a resonator. They don't quite it down a lot, just a little but has very little effect on flow. Most standard mufflers force the gases though a screen and/or little maze to make it quieter. I'd say go to an ATV junk yard and buy 2 mufflers from atvs that are straight/simple to modify, like the 250es/sx style mufflers and stack them. It will be just a whisper of air. I've seen that kind of setup for hunting machines and the guy I talked to claimed he rode up on a deer and it saw him before it heard him. That setup was on a TRX350D 4x4 (stock pipe + a 2nd pipe clamped to the outlet pipe).
FYI, with the longer pipe and more muffler, you'll probably loose a little power and the carb jetting might end up being too rich. Don't forget to retune once you get the system setup.