You are asking a question I will not answer. I like them both, but I like them both for different reasons. And each of them has some weaknesses as well.
Quantar
Getting very old in the tooth. If you get one. Get one with the fan in the face of the power supply, not the one with the heatsink in the face of the power supply (the ONAN supply) The Onan supply when they get old they fail very drastically, with blue fire out the front. When it happens the power supply is done. Non-repairable, burnt traces off the board done. I have supported over 100 of these units that were 800 Mhz. The Power supplies are sort of fail prone, but with the number of 800 units floating around used good supplies are available,,, stock up if you get a Quantar.
I personally am a fan of C4FM (Astro digital or P25). I have never replaced an exciter or receiver in a quantar. Been working on them for over 10 years, way past their end of life. PA's do fail, but are typically repairable. If you go this route,,, be damn sure what you are getting. Get a copy of the correct part numbers for EVERY piece of the unit and verify ALL of it. The SCM (Station control module) is key to it operating. There were several and only some of them would allow for standard analog repeat. Also make sure that the range for all the modules match. A range 2 VHF amp and a range 1 exciter will NOT work together. And moving then from range to range is an undertaking. Some fools are piecing these together for spare parts and you may end up with different range modules if you are not paying attention. Range 1 is for ham VHF. There are 3 ranges that are common for UHF... range 2 is for UHF. Range 1 is 403 to 433 and range 3 is 470 to 520 so you don't want either one.
Try to get a v.24 card, and an astroTac or SpectraTAC if you want them to vote. And v.24 links back from RX sites are possible but require some Cisco smarts to make happen. And the links will be Ethernet.
MTR2K /3K units.
Range info applies to these as well. Know what you are getting
3k's will vote DMR. You can vote DMR with the right software and some old 8300/8400 repeaters with a firmware upgrade. It's done over Ethernet as well but sin't as complicated. They will also connect to a JPS or Doug Hall voter as well for analog voting. Audio link are needed and I will leave that up to you how that happens but again, Ethernet links are your friend and only require being purchased once and don't have reoccurring costs like having Internet to each site. EchoLink and the like are possible with DMR, but you do it with a control station and not directly into the repeater.
Both have Mixed mode ability,, but the DMR mixed mode requires a license from Motorola. The Quantar P25/ analog is native to the SCM.
Now as far as your receive issues.
First option is a pass can that is very tight. I would slip it in between the duplexer and the receiver. Yes, you will have insertion loss of about 3db but if you are having innermod issues and it's effecting the receive, fixing the issue by degrading the receive by 3 db is an acceptable method in the commercial radio arena. 3db on receive isn't as much as you think. And the only signals you are going to be missing were not very good to begin with. Beyond that is a crystal filter, but those are expensive and fragile, they will not take a surge well at all. Again, place it after the duplexer.
You may be able to cheat if you have several sets of duplexers sitting around. Steal a single receive can off another set and put it in line of the set you have. And while we are talking can's, what sort of shape are the ones you have? If they are some old set of whatever, that are 30 plus years old, they may need rebuilt. The tuning slugs are silver plated in most of them and can be cleaned up with silver polish. The finger stock can be cleaned up in a similar fashion. But you will need to take them completely apart to do it. So tread lightly if you are unsure how to do this type of work.
As far as the MSF kits. The RX bandwidth is pretty much based on the IF filter you used in the kit.
The kits were to convert a wideband radio to narrowband. And yes if you are running 25Khz signals through them they are cutting off a good bit of signal and causing the audio to sound bad. One option is to find the correct IF filters for 20Khz and install them in the receivers. That would address your issues.