That would definitely be something to check before connecting it… 
That is my nightmare, to think i have the polarities right but instead fry my board.
Get a multimeter! Even a cheap chinese one will work wonder. If you plan to do projects long term I would suggest a better quality one like from Lidl, there are alot of other better ones, like the fluke for 200€ but those are for professionals that use them for their job.
Those are like 3-4€ 
And for hobby electronics they are just great.
The Lidl ones are like this 
they are 18-20€ but they have more features and protection like a fuse.
I started with the first kind for years, and now im pretty happy with the lidl one.
Got the new battery setup. Here’s the battery case after I ground out the space:
And here’s the battery in it before I put the proper end on the cable:
And last but not least, Here it is in the gameshell with the old battery beside it for comparison:
Works great so far! I haven’t played enough to speak to the battery life but it charges without issues.
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Looks great! What’s the capacity of the new battery? And where’d you snag another battery module casing from? 
2000mah battery, I’ve got the amazon link a little up in the conversation. I bought two clockworks so I’ve got two of everything.
where exactly did you place the battery circuit ? And how exactly did you modify the battery ? Can you post a more thorough guide?
Currently Testing, but it looks like a 3DS XL battery may be perfect. 3.7v, 1750mAh, fits, cheap.
With a little bit of dremel work it looks like it would even fit in the battery module case (sans the battery board).
Been running CaveStory for 30 minutes with no issue so far. Will see how long it lasts. (Not actually playing the game, just leaving it running).
https://www.amazon.com/Official-Nintendo-Battery-Replacement-COMPATIBLE-Nintendo/dp/B06ZZNR12Q
(Not actually official despite the name, but at 8$ USD might be worth it. Purchasing one to test with so I don’t have to keep using my real 3DS XL battery)
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Running CaveStory:
GS Battery (1200 mAh) = 2h 55m
3DS XL Battery (1750 mAh) = 3h 40m
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that’s a nice increase in battery life. i’d like to see how it compares to 1500 mah nokia batteries on amazon.
After the last battery change to 2000mAh I did some more measurements to see if I can get a bigger battery in my second gameshell. This one appears to be a size that will fit with some mods to the battery module:
https://www.amazon.com/gp/product/B07BTR57S4/
I’ve ordered it and will see if I can get it into the battery module. I’ll post picks after I put it in.
Ordered 2500mAh from Adafruit off Amazon. https://www.amazon.com/gp/product/B01NAX9XYG
—Updated Battery Times—
Running CaveStory:
GS Battery (1200 mAh) = 2h 55m
3DS XL Battery (1750 mAh) = 3h 40m
Adafruit 328 (2500 mAh) = 5h 23m
Note: The settings I am running with are backlight brightness at 2 with wifi on. When I checked amp draw, those were the two biggest factors. No other settings had a significant change for draw that I could tell. With Wifi Off the times may be higher, and With brighter backlight may be lower, etc, etc.
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does it fit in the gameshell battery case?
Not without some dremel work, which I did not want to do (It should fit though if you’re okay hacking the battery module case). I just placed a paper spacer so everything fits properly and the battery doesn’t shift when the unit is closed.
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Also, I used the connectors QuantumKraken posted (Swapping out Battery for Larger Capacity Li-Ion?), and yes, they do need to be connected in reverse. Black to red and red to black (But always ensure correct polarity anyways).
how come you need those additional connectors for the battery? based on the picture of the battery it looks like the same connector used by the gameshell battery?
The connector the battery comes with is not the same size connector. Battery has 2mm 2 pin jst connector, gameshell needs 1.5mm 2 pin jst connector.
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Oh I see. Is it difficult to replace the pins on the other battery? I figured the cable is secured to it and couldn’t be replaced. I haven’t modded anything like that before
It is not too difficult, although care should be taken. Just use wire strippers to strip the tips of the battery wires (don’t touch them together as this will short the battery and can ruin it), and solder the new connector, ensuring polarity is correct (as stated, the specific connectors used are reversed so black to red and red to black. This is not always the case though and you should double check the wires are going to the correct places, and/or use a multimeter to triple check).