Speaker crossover mod. Your advice?

You may want to consider starting from 'scratch'.
Get a schematic even if you have to start tracing wires around.....

That board has (GASP!) 5 iron core inductors. In the Magnepan world of DIY, that is one of the first things to go.....change the iron core to an AIRcore inductor to eliminate possibilities of saturation.
Any series resistance changes can be made up using lower or higher resistor values.
Gotta have the schematic, first, though. Start tracing where the wires come TO the board from the amp.

Also, any new caps are likely larger than stock. It just seems to work out that way.

'Bypass' caps have a following, too.
Caps in parallel add value, so if you need 3.6, you can use a 2.7, a 0.82 and a 0.1 equalling 3.62 which is 'over' but well within the tolerance.
The stock caps are probably 10% and the Clarity MR are 5% which puts you within design intent, even 'worst case'.

Looking at the picture of the board, the inductors are not in the best configuration.
ALL inductors should be at right angles to one another.....never parallel or coplanar.

The new caps will be GIGANTIC compared to the stock caps, so be ready. Look at the data sheets to get an idea how large the new caps really are and be ready to work with layout. Good idea going external, 'cause frankly, you probably don't have room IN the enclosure for the mods you have in mind.

Custom made caps? Not a bad idea, but I'll bet they cost $$$$

More capacitor tests than you'd have thought possible.....
http://www.humblehomemadehifi.com/Cap.html

conclusion? Try for yourself.

Eld is correct. L6 is a roadblock inductor.

You might want to consider an all-new layout with point-2-point and terminal strip wiring.
You should change those nasty iron core inductors, too.....at least for the bass and possibly the midrange.

How many layers of conductor does the board have? IF a single layer on only 1 side, just drill and AVOID any traces. IF conductors on both sides, you'd best be REAL careful.

Did you go to the Humble Hi-Fi site? The site 'owner' DOES mix caps with claimed good results. This guy has tested multiple dozens of caps and has a fair grip on the subject matter.

Just an example, the caps in my crossovers have 4 in parallel to get the required value.
mag16-2.gif

Listen to Al.

The advantage of multiple caps in parallel? Lower ESR.

The DIS advantage? Lots of space. And, since caps are not 'pure' capacitance, they also have an inductive AND resistive component. Careful consideration must be given such changes.

Changing the caps without addressing the inductor is only 1/2 the job. if that.

Caps are also considered microphonic, which is a good reason to get the crossover OUT of the enclosure, not to mention the increased volume taken up the the caps could conceivably change the bass tuning.

Get an integrated plan together.

NO inductor change recommendations? hmmmmmmm.

I made a big post about 'parts ain't parts' and it never made it.

without elaboration:
no part is pure anything. Inductors? have DCR and capacitance.
Caps? ESR and inductance. Caps are even microphonic.:: Clarity link available upon request.

It is possible and not THAT tough to replace a saturable small ga. iron core inductor with an aircore of similar (within say......5%) DCR. My Maggies have an iron core inductor. .4ohms, 16ga. wire. Online calculators? Designed a new inductor of 0.38ohm, using 14ga wire.
IF the minor effect of a change in DCR is of importance than surely the configuration of the inductor must be important, too.

The OP of this thread? The crossover had 7 inductors and they were not optimally placed....mutual inductance, and all.
I'd take this opportunity to go to an external crossover.