"Rather than acclimatize along the MT camping at Outpost and Trail Camp, I would like to look for a new backpacking route that would also achieve gradual acclimatization. I would like the trip on the trail to last three days and finish at the Portal. Any recommendations on where to begin and paths to travel?"

Brent, sad to say, there is no such route. The problem is that the main trail is about the most direct trail route possible. There are other routes, but they are definitely mountaineering routes, needing skill.

Also, the MT is about ideal, from an altitude profile standpoint. The Cottonwood Pass/NAP route drops you down until the last night at guitar lake. Plus, you have a real problem if you have to bail. I don't think I'd like to have a "no bail" route, in the situation you describe.

With the 3 day window, you really have no option but the MT.

So, how to optimize?

I agree, getting some "high time" on SoCal mountains would help. You don't have to get over 10k to see a lot of benefit, but I'd say you want to get to 8, if you can. Spending a sat night at the Sierra Club hut on Baldy at 8200 would make a difference, particularly if you could do that a couple of sats in a row.

Taking the tram up San Jacinto, then hiking into one of the camping areas would be a lot more effort, but would do the same.

The South Fork Trail up San Gorgonio to Dry Lake (9,000), is another option.

I've done them all, and they're all fun in their own right. You might mix and match for variety. It does seems like about a month is the limit for protection from acclimatization to endure.

I also suffer from AMS, more than average. I always start my hiking summer at Horseshoe Meadow for a couple of days. But it usually takes a month of weekend trips before I am free of symptoms. I can really relate.

Oh, one other comment. Your start time from Trail Camp of 3am is VERY unusually early, and in my mind, unnecessary. I have no studies to back this up, but I believe sleep deprivation is significant contributing factor to failure to successfully summit this mountain.