I’ve not built a Two Stroke with the Pentode/Triode switch but here are some ideas.
Assuming that you’ve optimized the 6.3v filament circuit with the techniques outlined here: http://www.valvewizard.co.uk/heater.html
then check out this page:http://diyaudioprojects.com/mirror/members.aol.com/sbench/humbal.html.
Note that if your PT has a center tap for the 6.3v, you could not add an artificial center tap. If you do have an artificial center tap, using resistors that are matched to the same value will maximize the humbucking benefit (or use a balance pot instead).
Although SE amps have a reputation of being noisy, the Two Stoke can be a VERY quiet circuit. If your amp has any hum in pentode mode (other than a very slight hum from the PT), you should resolve it and see if it reduces the triode mode noise issue.