Wow thats a bumer that a kit that cost so much is not desiged that well in that one of the most important components,the one that is used the most, is super critical in operation and keeping one from having to go swiming for it lul,is so hard to just bloddy change.
I would see if there was any other way to get to it but if you have to cut open the hul then so be it its done on the full scale subs since its a bit tugh to sqeeze a reactor by the hatch.

It should come out realy nice though , added weld lines never hurt.

I noticed that problem in my Gato also and right away decieded way before I ordered the sub that I had to redesigne the internals to my standards that as a hole the the entire internal casing must come out  so that the above would never occure.Its only common sence to be able to gain acsses to the motors and any other impotant part of the sub if not it becomes an expensive papper wieght and a pain to just replace the motor.
Fotunatly the Gatos full open hull is a breeze to modify, anything can be installed in her but with other closed hulls a difernt aproach though similar outcome must be made to make it simple to service this great sub. 
I would if I where you would be to gut out the sub and make an Aquacasing for her,i know that is alot of work but in the end its worth it.  </p>