It depends a bit on what type of generator and regulator you have. With the simple and stupid cut out on the 3 brush splitdorf generator it is the battery size (amp hours) that is a vital part of the charging system. And it has to be an old type wet lead battery. The internal construction of the generator determine that because the field coil is using the battery in symbiosis as a buffer, up to a limit. A smaller battery (and even orig. battery) it at a greater risk of boiling out. 

Orig. battery is at (was it 19AH or 16?) However, that is probably of larger capacity of any of the modern batteries you find today on the market that will fit the battery box.

Slightly better chance of preserving the battery is with the 2 brush Bosch generator and regulator that senses and regulates the current that goes to the field coil. It is possible and I recommend to modify the Splitdorf to a 2 brush system with a sensible regulator.

Best chance to preserve a wet lead battery and even run with smaller capacity batteries, perhaps even sealed or gel batteries, is to use an electronic regulator that is a lot quicker and more sensible to the draw and what the battery can take in regard of charging current. There is a few on the market, both for the Splitdorf and Bosch. 

A fair warning is entitled. Regardless if you use an old generator or decide to run some of the alternators that is small enough to fit on the Indian, a standard electronic regulator is not suitable for a modern fancy metal, ion hydrid or hybrid battery variants that is easy accessible on the market these days. Those kind of batteries needs a specially adapted for the type of battery, fast acting and exact electronic regulator. The batteries could be fire or exploding hazard when overcharged, as also gel batteries are in some cases. BUT I don't know if such specialized regulators are available on the market for those needs. 

So, a wet lead battery is most common to use. Today's batteries is more delicate constructed with thinner plates and stuff inside so they are prone to vibrate to bits and short out internally, in the battery box. With a hard tail as the 101 is, the jolts and vibrations are tremendously violent on the pot hole riddled roads of our "modern days"! Use a tilers knee pad under the battery and loosely on its sides to isolate from vibrations. I even made a coil sprung pad under the battery in order to have a longer shock absorption range!! Still the crappy batteries of today doesn't last long...

I have Gene Harper's electronic regulator with a small cheap sealed (AGM) battery, which has lasted forever.  These batteries are much more rugged than a flooded battery because the plates are sandwiched tightly between glass mats.  They can't tolerate overcharge for long because the tiny amount of electrolyte will soon be lost.  I would not use an AGM battery without an electronic regulator.