Question: I'm wondering if there is any research about if there are better, or at least "not so bad" times of a child's development for a father to less available. (Not completely absent, but time would be limited to weekends and a bit most/some evenings on weekdays.) 

Situation is a two-parent household with one 3 year old daughter. I have the option for a rather high-paying job, but it would require excessive (to me) commuting, like 2 hours each way. If it were temporary with the goal to move closer, it would be fine, but in this case it would be at least 6 months, likely a year.

Answer: 
Based on my experience as a military kid, my husband's experience as a military dad, and my experience as a foster parent, the biggest factor is how the limited schedule is presented to the kids. For smaller children, like your daughter, they tend to quickly adapt to the new normal, as long as the parents are satisfied with the way things are, and are available to the kids when they are present. If the parents tend to view the schedule as something negative that they need to apologize to the kids for, or make up for by going overboard in the time they are together, then the kids will cue off that. 

As a side note, the schedule you describe (weekends and a little on weeknights) is fairly common with small kids and working parents. My husband and I both work, and I get weekends and a few hours on weeknights between picking the kids up at daycare and bedtime. My husband gets even less, as he works later, and the kids are well attached to both of us.
Simple answer, no there isn't a better or worse time in general. Each child is different and is going to need different amounts of time. But if you think about it, a great many children don't see one of their parents during the week very much. I work a typical office job (8-5) but if there's a late night, which happens in the professional world, I don't get to see my kids that night. I don't let it bother me: they're in the very capable hands of my wife, and they know I love them very, very much.

What I would recommend is trying to shift your schedule. Your 3 year old daughter probably has a bedtime of around 7pm, right? If you were to go to work for your 8-5 job you're going to get home just as she's going to bed. This job is going to be *very* taxing on you. A typical 9 hour job is going to consume 13 hours of your daytime. Count half an hour at morning and night and you're only looking at 2 hours of leisure time per day for those six months. That's demanding!

If you could shift your schedule to be 7:30-4:30, you'll at least get half an hour with your Daughter. You also could try to work out one night a week taking off a bit early, or working from home that day, to get a little extra time with her. And don't forget, Mom will want a break too, and she'll want you too! You'll also need lots of dedicated time with Mom to talk about how Daughter is doing and what she's up to. And don't forget this schedule means you're *leaving for work* at 5:30am. Yikes! Get that move done as soon as possible!

All this means you're going to be very tired come the weekend. But the reality is that's going to be your only time with Mom and Daughter, so you have to make the most of it!

If I had to wager, I'd say that in terms of development and building that lasting relationship, a child realistically isn't going to see a difference between half an hour with you on the weekday and an hour with you on the weekday. Especially being three already, chances are she has such a strong bond with you that even going for a few days at a time isn't going to have a major long term impact.

tl;dr

* Don't worry too much about it. You'll just pass that worry on to Mom and Daughter.
* Take steps to work schedule so there's at home time with Daughter.
* Get a hands free setup for your car - CALL HER multiple times a week on lunch breaks or on the trip home. If you can skype or facetime, that's even better. (Doesn't have to be every day, but a call from Daddy twice a week will go a long way!)
* Stay up to date on her development and be involved with the time you have.
* Don't overwork yourself - it will make what little free time you get suck.