At the moment I have a wAP R with a cat 4 miniPCIe Huawei modem.
Then please do checking BTS of your ISP and list the Bands, connect via all bands your ISP and check what one band-s have a biggest speed.
On the wAP R product page
only the R11e-LTE modem is listed as related product.
Would the new R11e-LTE6 modem be a suitable drop-in replacement for the existing wAP R modem?
Yes, he have got a miniPCIe socket and you insert Huawei modem, you can insert other modem's too. Check post-s at this forum and wiki hardware list. The MikroTik modems will be work.
I think the antenna u.FL connector are standard and you can use the same pigtail to SMA for connecting external antenna.
As the design of the wAP ac LTE6 kit appears to be the same as the wAP ac LTE, does this apply to the antenna design as well? And compared to the wAP R?
FE -> GigaBitEthernet, wifi n -> ac but the same socket mPCIe for modem with the same internal antenna.
I.e. would LTE performance be better with a wAP ac LTE6 kit compared to a wAP R with R11e-LTE6 modem or the same?
I use SXTR with R11e-LTE6 and have connected B3+B8 and even be 600m from my BTS my ISP give me max 75/40Mb then my theoretical limitation at 100MbEthernet ports are not limitation. Carrier Aggregation give you little more speed but a lot more stability.