I feel like you're making unnecessary work for yourself with your engine placement. If it's placed where it should go, you should have more than enough room for the stock TC and stock trans shifters.
My setup is set 1/2" forward over your engine. I wasn't comfortable with the amount of firewall clearance I had so I decided to move it forward. One of the header bolts on the driverside was ~1/8" from the firewall not to mention the coil pack that was really close to the heater hoses. I'm much more comfortable with the fitment now.
The stock TC linkage (as I mentioned) is a bit in the way so I just got rid of it and ran a direct linkage which really only took me an hour to fab together using an NP231c TC lever (but you can use an NP231j lever flipped and cut). This will give you a direct linkage that is much simpler than stock, and much smoother to shift.
I had the boostwerks shifter which is a direct linkage. I couldnt get it to shift the TC smoothly in its current setup. It was too extreme of an angle from the shifter to the TC shift selector. I experienced how smooth the shifts were, it was great. I just dont feel like fussing with it. The cable shifter will be simple and it will work with just about any transmission mount i use.
The stock trans shifter I'm not really sure where you're having an issue, as the driveline length shouldn't have anything to do with it as it's cable driven. I could move my engine forward or backwards a foot or 3 and still have no problem with the stock trans shifter, cable, and cable mount on the trans.
It doesnt look like you're using a stock trans cable. Mine barely reaches the shift arm let alone making a big zig zag with it. Your probably using a 5' blazer cable or something.
I did use a stock rear driveshaft on the rear for a month or so without issue, and that was with my rear axle set back almost an inch from stock location, with 6.5" lift, and I believe the D44 pinion is a touch shorter than the 8.25 as well. I feel like if your t-case won't reach the rear pinion with a front DS, your engine is way too far forward.
The front DS was about 2" too short (in the rear). Maybe I'm not extending it all the way, but its no big deal. I want new driveshafts anyway and I already accounted for the cost.
On my setup, getting the motor IN was the hardest part, simply because the lip of the firewall was in the way. I pounded the lip back/down about an inch (so it's almost flat) right behind where the 4.0L valve cover would be. From that point on, everything fit very nicely.
The only fitment issue I ran into was with the stock XJ trans shifter. Regardless of how you set it up, the stock cover isn't long enough to drop all the way from park to 1st. I feel like I could've found a way around that by modifying the trans shifter lever length (on the trans) to adjust my overall throw, but my center console was sorta bunk anyway and I just removed it.
I wont be removing my center console. I might just order the winters shifter and make it fit, but I'm going to hold off on it for now. I'm going to deal with the shifter situation later.
I know some of the aftermarket shifters have adjustable throw which would solve that problem, but they probably don't fit in the tunnel. All I did with mine was modify the detents in the shifter to match the 4l65e trans shifting pattern (which I did mostly with an angle grinder and sawsall).
Maybe post some pictures of the fitment issues your'e having?
I'll post some pictures of the driveshaft clearance later in the week, thats really the only issue I'm having with fitment of the combo.
. You've got a much cleaner build than mine and I understand differing priorities. Just seems like you're making more work with the motor sitting that far forward, when pushing it back a touch doesn't have any negative consequence. With extreme torquing, I'm having no clearance issues. Was just a bitch to get it in 
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