Auto to manual conversion. If you could do it over....regrets, pitfalls, long term opinions???

I've done it both ways, and liked it both ways.
There are good reasons for either set-up

But when swapping to a manual,with a mild engine, or a teener or smaller engine, I highly recommend a 5 speed. The ratios are closer together, so the engine can stay on the power longer, and it will seem bigger,more powerful than it would with fewer gears.
But for a streeter, with a 65mph limit, pretty much anything will get you there.
And when swapping to an automatic, you get the advantage of TM (Torque Multiplication) inside the TC, which allows you to use a little less rear gear. Unfortunately, the 1-2 shift loses a lot of rpm, so to get back on the pipe, a different cam is often a good idea.
And the nice thing about a clutch, is the adjustable "stall". Just rev it up until you get the power you need to suit your mood. You won't be limited by the TC.
So; I have had tons of fun with either.
But the most fun I have is when the combo is geared to hit 65mph at the top of second gear, at the shift rpm. We gave it all she's got, and there ain't no more.
Unfortunately, this will take completely different rear gears,(auto or stick) and the automatic should really have a wider LSA,(really the stick could have a tighter LSA), and, for a streeter, it is often better to work backwards from the rear gear demanded by the application.
What I mean is, if the car is gonna spend a lot of time on the hiway, a 2.94 rear gear might be the biggest acceptable gear. But a guy might have a teener with a 268 cam. The shift rpm of that 268 might be 6600 or more. Well that makes the top of first gear(2.45x2.94) to be 70 mph. Well that doesn't look that bad, until you figure out that the engine doesn't wake up until 3500 at the earliest, which is 37 mph. Can you say s-l-o-w out of the gate. So this combo needs a fairly hi-stall TC to get off the line briskly. Couple that with the typical 110LSA and whenever the engine is out of the powerband it's kindof slugish.And finally, the hiway cruise rpm is a theoretical 65=2375 with zero-slip. So having a 3500TC in there is probably not the best idea.
But the same combo with a 360 and a stick is a different beast. Firstly the 268* is a better fit in this engine of 42 more cubes.Secondly the 110-LSA is a better number for a stick car, cuz the rpm-drop on the 1-2 shift is much less. Thirdly, you won't have to rev the engine as high to stay on the power.And most significantly, you have the adjustable "stall".And finally, 65mph will be 6315 rpm at the top of first, meaning the powerband is all used up. And if she's slow out of the gate, just slip the clutch! Deliver as much or as little power as you need, no waiting until 37mph for the engine to wake up.
But if the cruise rpm is not an issue, then you have much more freedom in the combo.
For instance; that teener with the 268*automatic will be dynomite with 5.38s.These will get you 65 at the top of second(1.45). And the powerband will start at about 3600, so with a 3600TC, the power band will start right on the line,lol.
Consider same engine with a 4-gear. This combo will like 4.10s to hit 65=6324rpm,at the top of second (1.91) gear. And if you slip it out at 3600 that is the fast way. Of course 4.10s will cruise at 65=3310 vs 4344 with the 5.38s,heehee.
So, as you can see, there are advantages to both.

But lets say you had a 5speed stick on that teener. It might have a 3.24 low in it and it might have a .68 od in it.With this combo you could run a 3.73 rear and probably end up at 6175@65, all used up. So then you could give up that 268 for a 262 and grab a little more torque throughout the lower rpms. And the OD would get you 65=2048;sweet.
Of course now you could re-gear it to run 65 in third gear...... and put still more average hp down from zero to 65 mph. This would allow either a smaller engine or less cam for the same performance level.But 65 might now be 2900ish.

Similar results can be had with a 4-gear automatic; but not quite as dramatic.