Engine/ Trans Combo?

As to question 2; yes this combo will work together.
As to question 4; You kindof need the bell house that fits over that 5.125 retainer, which means everything else that goes with it as well. There are others that can be made to fit with some machining.
As to question 3;
That od trans has ratios of 3.09-1.67-1.00-.73od.. When you shift, the rpm drops are to 54%-60% and 73% ..
To build a 400hp 360 is gonna take a mighty big cam, to put the power-peak up around 5600. With a shift rpm around 6000.
When you shift into second the rpm will drop from 6000 to 3240. The torque peak doesn't even arrive until maybe 4100 or more. So, usually, that trans is a bust for a hi-rpm, narrow powerband engine.
For a streeter;
That combo is gonna want rear gears in the high 3.xxs, say 3.91s, to 4.10s. The 3.91s gives you a starter gear of 12.08, so that's kindof high but you need it to overcome the 1-2 rpm drop as shown above. So now, with 27" tires. 6000 in first will get you 40mph. The torque peak in second will come at around 4100 so that's 51mph. What's that big-cam engine gonna do from 40 to 51 mph; now in second gear? Well it's a good thing she's in a light-weight-A, so it won't struggle too badly.

But that's not the worst of it. Keeping the 3.91s and the 27s; and going for a leisurely tour; which is gonna be about 95% of the time; a comfortable place to shift,for me, is about 2800rpm. My pipes are singing and the engine is sweetly pulling. The trouble is that on the 1-2 shift the rpm will drop to 1500. And if you've ever had a 400hp big-cammed, manual-trans, 360, then you'll know that this is a bit of a problem.
Firstly; the engine has very little torque down there, so it's gonna take a lotta throttle to keep accelerating from what is now ~19mph.
Secondly; but your ignition timing might already be 20/25 degrees. And depending on your chamber design, this could put you smack dab in the middle of detonation, so when that happens, you have to back off the throttle until it quits.
Thirdly;So then you take out a bunch of timing , and turn second gear into a dog-gear until 3500rpm@43mpg..
So what's the solution? Well;
1) you could just run first gear up high enough so that it drops into second at some above-detonation point ..... but that is 43mph@6400rpm; so that's not a good option. Or
2) You could build the engine and fuel it to be detonation free with a delayed timing curve. Or
3) some combo of the above two. Or
4) get rid of that PITA box that doesn't like this combo. Been there/done that.
The problem with that box and a hi-rpm cam is that second gear is so very far away.
In my experience, a nice second gear to the road with a 400hp 360 is about 6.80/7.00. To get that with that box will require a rear gear of 6.9/1.67= 4.10s . Now you just have to figure out how to get into that gear at a high enough rpm, so the engine will have the torque to pull it. Or you need to build the engine for torque. And that means you need to keep the cylinder pressure up, which means some combination of an early-closing intake and a lotta compression ratio. And that usually means throwing out the 400hp target.

But if you get yourself a Commando 4-speed, with ratios of 3.09-1.92-1.40-1.00, then the 400hp combo is back on the table; I know it works cuz that's what I got.... in a 3650# 68 Barracuda. And I run it with 3.55s for a starter of 10.97 which easily gets me into 6.82 second gear road-gear. Do yourself a favor and use aluminum heads and crank up the pressure to at least 180psi. With this combo I run a 230/237/110 cam and full timing of 32/34 at 3400rpm on 87E10, 100% of the time. Idle-timing is just 14* to keep the low rpm from getting too jumpy.
And I highly recommend a dash-mounted, dial-back, timing delay,box. With 3.55s the minimum roadspeed is 750rpm =5.5 mph. But with 180psi cylinder pressure and idle-timing of 18*, the power pulses will be so strong,that in a second or two the entire car is gonna begin to go into donkey-kick mode. The best cure I have found for that, is to retard the idle-timing ( I run 14*) and make sure your Transfer-slot exposure is set just right, so that when you retard it to ~5* with the dial-back, it will run at [email protected] mph. Now the power pulses come waaay later with the piston already waaay down the bore, and running away from the flame. Mine will pull itself like that on a flat,level,hard, surface. And that's with 295/50-15s@24psi and 3650 chassis weight.

I have tried EVERY A833 ratio Mopar ever made (not including the Hemi-stuff), and for a streeter,the Commando box is the one to get. And with the various boxes I have run; I have also run every rear gear from 2.76s to 4.30s except not 3.73s. And with the current 230 cam and Commando box; the 3.55s are more than adequate. I actually like 3.23s a lil better. But the 3.55s get me a lil closer to the rpm I want at 60mph in second gear. 3.91s would be perfect to top out at 60=5600, but I broke mine,lol.

But I gottatellya;400hp in my 3650 chassis is waaaay overkill. I can't imagine it in a chassis ~400/500 pounds lighter.
Happy HotRodding

PS-1; to get to 400hp you will need long-tube headers and a free-flowing dual exhaust; log-manifolds are not an option for a streetable-cam. Early-As are notoriously hard to fit both headers and a clutch linkage. Be forewarned you may be in for some headaches, or sacrifices. I love my manual trans combo, so I would go for it. Jus saying.
PS-2; If you cannot find a Commando box for a reasonable price, then, I see the regular box in a lightweight-A as an option. The only difference is the swap of the 3.09 low for a 2.66. It will be fine.