I think you're wise to get it aligned with the new tie rod in; perhaps others disagree with me, but it is not as easy as it sounds to turn the new tie rod to the precise length of the old rod; plus, even with other components still okay, they've still got some micro-wear, so the old tie rod length is not the correct length. When I replaced a tie rod on my 220D last Fall I had to drive 20 miles to get it aligned and what a difference it made even though I had went to effort to set the new length equal to the old length.
Sorry for an old war story on greasing suspension components, But; back in the sixtie's a lot of the Detroit Iron cars came with a plug where the grease zirk would go, I guess to save a few pennie's. I worked as a mechanic at the time so when a car would come in to be greased I'd remove all the plugs and replace them with zirks. There was one fellow, who took very good care of his car, who insisted the zirks be pulled after greasing & replaced with the plugs. So, I did it. He was a good customer and I'd argue with him every time that it was costing him half an hour for no good reason. I'm not a fan of the new components that are sealed and require no greasing. Dust/grime, I would think just has to make its way inside the boot. In the old days, in my opinion, greasing through zirks had less to do than ensuring there was adequated grease beneath the boot than the driving out of the old dirty grease. One had to be very careful if a customer had not had the car greased in a long time, or ever, as the grease tended to harden near the lip of the boot, so the pressurized grease would break the boot. To me, the new greaseless ball joints or king pins is less problematic than the pressed U-Joints. Years ago if one of my cars didn't have threading for a zirk I'd drill & tap it. Not that the grease would ooze out, but to force out old hardened/dirty grease. I say all this as opinion as I've never read of studie's that compared the old zirk style with the newer sealed joint systems. I'd be very interested to hear anyone's opinion on this.