Something is definately blocking your charge rate. I have a similar setup to the one you are contemplating 400a/h batteries, 100a alternator, Sterling regulator. even when topping up the house batteries with less than 50a/h used so at about 85% charged I get 50-60a initially falling to about 30a untill the regulator cuts down to 13.8v. The alternator is frequentlyputting out 70-80a at 1500rpm at these charge rates as it is also charging the electronics battery, start batt and running the ship.
The question they is why is your alternator not achieving close to its max output? It could be a problem with the alternator, often the drive pully is to small so the alternator is not turning fast enough. Ideally you should get max output at about 2000rpm so if your output keeps increasing as the reves go up much beyond this the the pully setup might be wrong. The other problems can be poor battery condition, how old/good are the batteries. Poor wiring/faulty connections, check the voltage at the alternator output compared to at the battery terminals, after taking out any drop accross a diode spliter if you have one you should have neglagable volatage drop at 25a.

If it was me I would hope to find out what is wrong befor changing the alternator sothat you know what else to change, otherwise you could spend all that dosh and get little improvement if it is for, example your wiring strangling the output. If you do change to a 100a+alternator you WILL need to do a fare bit of rewiring as the cable will need to be abot 8mm dia accross the conductor with some serious terminals, ordinary crimps wont take 100a!!