A 35A auto-type alternator will only put out.....
about 2/3 of that nameplate 35A rating. This is due to the industry practice of specifying the output as PEAK amps and not RMS (or average) amps. Given an alternating current waveform inside the alternator, the internal bank of six rectifying diodes will deliver the rectified DC output. However the average or more correctly the Root-Mean-Square (RMS) value of that current will be only about 2/3 of the peak. Hence, 2/3 of 35A is about 23.3A of DC current.
AND, that maximum value will only be observed if the alternator is running flat out (otherwise known as full-fielded). If the internal regulator is throttling back the alternator you will see less current.
To put this in the real-world perspective, suppose you have a battery bank of two group 24 deep cycle batteries. I think these have about 90-100AH of capacity each. In parallel you would have about 180-200AH. At a 50% discharge you would be trying to replace about 90AH into the batteries. If your alternator could run at max output (and it can't BTW), it would take over four hours of engine running to recharge fully. Don't forget that due to charging inefficiencies you need to replace about 5% more AH than you took out.
In short, you may have a perfectly good alternator but realistically under-sized for your recharging task.
Any decent auto electrical shop can test your alternator in a few minutes and tell you what if anything is deficient. Beyond that, I think your solution will be a larger alternator that is designed for continuous high output, and MORE importantly, an external regulator that is actually designed to recharge deep-cycle batteries.